Coefficient Of Genetic Differentiation Research Articles

Molecular characterization of diversity in Annona squamosa L.: A high value tropical medicinal plant

Introduction: Annona squamosa L. commonly known as custard apple, is an important under-utilized fruit species from tropical and subtropical parts of India with high potential as commercial horticultural crop. The aim of this study was to determine the genetic diversity among populations spread across districts of Udaipur, Rajsamand and Chittaurgarh falling within Aravallis in Rajasthan. In all, 21 populations were identified and subjected to molecular evaluation using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers. The cumulative analysis carried out on the basis of RAPD and ISSR data sets revealed 73.91% polymorphism. Methods: A total of 251 amplicons were produced using 19 RAPD and 15 ISSR primers. The pair-wise distance matrix calculated by Dice’s co-efficient showed a distance range of 0.67 to 0.95 when computed using cumulative data set. Results: Characterization of genetic diversity within populations based on combined data set showed that percentage of polymorphism bands (PPB) ranged from 29.19 to 50.93. Nei’s gene diversity (HE) values varied from 0.1002 to 0.1964 within a total genetic diversity (HT) of 0.2509. The average observed number of alleles per locus (Na) was 1.3602 and Ne was 1.2400. The Shanon’s index was 0.2002 (Hpop) and 0.3800 (Hsp) at population and species level, respectively. Conclusion: The moderate gene flow value (Nm=0.59) and significant coefficient of genetic differentiation (GST=0.458) revealed low level of genetic diversity within population and highly significant genetic differentiation among populations of A. squamosa. The UPGMA dendrogram resolved all the 21 populations representing 3 districts into various clusters according to their genetic distances. The principal component analysis (PCA) supported the UPGMA results and justified the relationship among populations.

Genetic Diversity and Structure through Three Cycles of a Eucalyptus urophylla S.T.Blake Breeding Program

Eucalyptus urophylla S.T.Blake is an important commercial tropical plantation species worldwide. In China, a breeding program for this species has progressed through three cycles but genetic diversity and structure in the breeding populations are uncertain. A sampling of field trials from these populations was carried out to evaluate their genetic diversity and structure using 16 microsatellite loci. Significant deviations from Hardy-Weinberg equilibrium were recorded at all 16 loci in the populations. Overall expected and observed heterozygosity (He and Ho) estimates of 0.87 and 0.59 respectively for the first cycle population, and 0.88 and 0.60 respectively for the third cycle population, revealed reasonably high levels of genetic diversity. The genetic differentiation coefficient (Fst) revealed low differentiation among pairs of provenances (from the species’ native range) comprising the first cycle population (range: 0.012–0.108), and AMOVA results showed that the majority of molecular genetic variation existed among individuals rather than among provenances for the first cycle population and among individuals rather than among field trial sources in the third cycle population. Levels of genetic diversity appeared to remain unchanged from the first to third cycle populations, and the results indicate prospects for maintaining if not increasing diversity through recurrent breeding. Likely effects of artificial directional selection, prior to sampling, on both populations examined are discussed along with implications for future E. urophylla breeding.

Assessment of genetic diversity in Salvadora persica L. based on inter simple sequence repeat (ISSR) genetic marker.

Studies on the genetic variation in marginal populations and differentiation between them are essential for assessment of best gene conservation strategies and sampling schemes. In this study, ISSR markers were used to establish the level of genetic relationships and polymorphism 50 genotypes of Salvadora persica collected from 6 different regions of Hormozgan province. The ISSR analysis with 9 anchored primers also generated 105 scorable loci, of which 85 were polymorphic (80.95%). Parameters of genetic diversity and its partitioning were calculated. The genetic analysis demonstrated that S. persica maintain relatively high genetic diversity (PIC was 0.63, Na was 1.27 and Ho and He were 0.15 and 0.17 respectively). The coefficient of genetic differentiation among populations based on FST equaled 0.20. Genetic identities between population's pairs were high (mean I = 0.88). These values are high as compared with other widespread congener species. Cluster analysis based on the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) revealed 3 main clusters for the ISSR data. The levels of genetic diversity maintained within populations of S. persica indicate that an appropriate sampling design for ex situ safeguarding should capture the majority of genetic diversity found within these taxa to help ensure the long term viability of this species. Furthermore, it could be inferred that ISSR markers are suitable tools for the evaluation of genetic diversity and relationships within the Salvadora persica.

ISSR and ITS analyses to assess genetic diversity and phylogeny to conserve an endemic and critically endangered tree, Memecylon subcordatum, in India

Abstract Memecylon subcordatum (Melastomataceae) is an endemic and critically endangered species of the Kalakkad-Mundanthurai Tiger Reserve in India. Twenty five inter-simple sequence repeat primers were used to screen 86 individuals. Nine primers produced a total of 61 bands (6.77 bands primer−1) ranging from 200 to 1900 bp wherein 48 bands were of polymorphic. Polymorphism was 78.69% within the species, 26.60% within the populations and 7.41%–48.15% among the populations. Genetic variation varied from 0.3069 (within species) to 0.1182 (within populations). The poor gene flow among the populations (Nm: 0.3133) could be due to the genetic barriers caused by the tributaries of Tambraparani river. The coefficient of genetic differentiation between the populations (GST) was 0.6148. The Bayesian analysis, multidimensional scaling analysis and principal coordinates analysis grouped all the 11 populations under 4 clades. The Mantel test showed significant correlation between the matrices of genetic and geographic distances (r = 0.652, P

Mitochondrial signatures revealed panmixia in Lutjanus argentimaculatus (Forsskål 1775)

Mangrove red snapper, Lutjanus argentimaculatus is a commercially important fish. The genetic stock structure of L. argentimaculatus from Indian waters was identified using mitochondrial ATPase 6 and ATPase 8, and cytochrome b (Cytb) genes. A 842 bp region of ATPase 6/8 genes and 1105 bp region of Cytb gene were amplified in 120 samples from six different locations along the Indian coast and obtained 58 and 66 haplotypes, respectively. The high haplotype and low nucleotide diversity values along with mismatch distribution, Tajima's D and Fu's Fs analysis suggested a genetic bottleneck events or founder effect, with subsequent population expansion in L. argentimaculatus. Coefficient of genetic differentiation (FST) values was low and nonsignificant for both ATPase 6/8 gene and Cytb genes indicating low genetic differentiation in L. argentimaculatus which can be managed as a unit stock in Indian waters.

Research Article Molecular Characterization and Differential Interaction of Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans with Common Beans (Phaseolus vulgaris)

The common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli (Xap) and X. fuscans subsp. fuscans (Xff), is one of the most important dry bean diseases of bacterial etiology. The present work aimed to study the genetic structure among and within populations, and also identify the pathogenic variability of Xap and Xff isolates evaluating the horizontal and vertical resistance of the host. A total of 42 Xap and Xff isolates were obtained were submitted to molecular characterization by rep-PCR markers, and inoculated in the genotypes CNFP 10120, BRS Notavel, and Rosinha G-2, for differential interaction studies. In the analysis of genetic structure, the coefficient of genetic differentiation (GST=0.5154) revealed diversity both within and among the pathogenic populations, confirming the result obtained by AMOVA (FST=0.5198). Of a total of 51 loci, 98% were polymorphic, among Xap 59% and within Xff only 21% were polymorphic. In studies of pathogenic variability, diallelic analyses showed significant effects of the general combination ability (GCA), of the general aggression ability (GAA), and of the specific interaction ability (SIA). Therefore, seven races were classified through the differential behavior of all isolates in the three genotypes of bean.

Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

Quercus variabilis is a tree species of ecological and economic value that is widely distributed in China. To effectively evaluate, use, and conserve resources, we applied 25 pairs of simple sequence repeat (SSR) primers to study its genetic diversity and genetic structure in 19 natural forest or natural secondary forest populations of Q. variabilis (a total of 879 samples). A total of 277 alleles were detected. Overall, the average expected heterozygosity (He) was 0.707 and average allelic richness (AR) was 7.79. Q. variabilis manifested a loss of heterozygosity, and the mean of inbreeding coefficient (FIS) was 0.044. Less differentiation among populations was observed, and the genetic differentiation coefficient (FST) was 0.063. Bayesian clustering analysis indicated that the 19 studied populations could be divided into three groups based on their genetic makeup, namely, the Southwest group, Central group, and Northeastern group. The Central group, compared to the populations of the Southwest and Northeast group, showed higher genetic diversities and lower genetic differentiations. As a widely distributed species, the historical migration of Q. variabilis contributed to its genetic differentiation.

Genetic analysis assessed by microsatellites for a diallel mating design of two geographical stocks of the blood clam Tegillarca granosa.

To determine the potential for productive efficiency and genetic improvement in the blood clam Tegillarca granosa, four offspring populations (ZZ, ZK, KZ and KK) were produced from a diallel mating of two different geographical stocks (Z and K). The levels of genetic diversity and population structures of four populations were analyzed using 14 polymorphic microsatellites. The results showed that the mean observed heterozygosities (Ho) of reciprocal cross populations (ZK and KZ) was higher than those of pure populations(ZZ and KK). The largest values of genetic differentiation coefficient (Fst = 0.067) and Nei's unbiased genetic distance (Dc = 0.263) were between ZK and KZ, and the smallest (Fst = 0.020, Dc = 0.116) were between ZZ and KK, which revealed that the largest genetic divergence was between the two reciprocal cross populations and the smallest was between two pure populations. This study demonstrated that the reciprocal cross populations of T. granosa had an extensive genetic difference and improvement, which may be advantageous for future breeding studies.

Deciphering demographic history and fine-scale population structure of cobia, Rachycentron canadum (Pisces: Rachycentridae) using microsatellite and mitochondrial markers

Cobia, Rachycentron canadum is a candidate species for aquaculture, distributed across the Indo-Pacific waters to the southern Atlantic Ocean. Information on genetic diversity and population structure of cobia is crucial for sustainable utilization and management of the species in natural waters. In the present study, we used 14 polymorphic microsatellite loci and mitochondrial cytochrome b gene (980 bp) to investigate the genetic diversity and population structuring of R. canadum along the Indian coast. Microsatellite analysis suggests a relatively high level of genetic diversity of cobia in the Indian region, with a mean Ho and He of 0.76 and 0.73. The PIC was also highly informative (0.841), with a mean no. of alleles of 11.304. Hierarchical AMOVA and genetic differentiation co-efficient between the populations was found to be low, but significant (FST = 0.035, P < 0.001), indicating fine scale structuring in the region. Pair-wise FST, neighbor-joining tree, principal coordinates analysis, and Bayesian analysis depict three populations of cobia in Indian waters: two in the Arabian Sea and one in the Bay of Bengal. The mitochondrial gene analyses showed discordant findings in comparison with microsatellite markers. However, both the markers yielded no inference of historical demographic bottleneck. Multi-modal mismatch distributions and ragged index, non-significant Tajima’s D and Fu’s FS, and L-shaped distribution pattern of the allele frequencies, indicated the lack of bottleneck events of the species in the recent past. Based on mitochondrial gene analysis, the population expansion was inferred to have occurred 0.046 Myrs ago, corresponding to the late Pleistocene.

Morphological and ISSR molecular markers reveal genetic diversity of wild hawthorns (Crataegus songorica K. Koch.) in Xinjiang, China

The wild hawthorn species, Crataegus songorica K. Koch., is an important wild germplasm resource in Xinjiang, China that has been endangered in recent years. The genetic diversity of C. songorica K. Koch. germplasm in five populations from Daxigou, Xinjiang, China were evaluated based on phenotypic traits and ISSR molecular markers to provide basic information on resource protection, rational utilization and genetic improvement. The F-value for the phenotypic differentiation coefficient of the 33 traits measured ranged from 0.266 to 15.128, and mean value was 13.85%. The variation among populations was found to be lower than that within population. A total of 303 loci were detected within the five populations by 12 primers. Within 298 polymorphic loci, the polymorphism was 98.35%, showing a high genetic diversity in C. songorica K. Koch. The gene diversity within population, total population genetic diversity, genetic differentiation coefficient and gene flow were 0.2779, 0.3235, 0.1408, and 3.0511, respectively. Our results showed that C. songorica K. Koch. from Xinjiang has a high level of genetic diversity at both the phenotypic and molecular levels. Significant genetic differentiation existed within population and the differentiation trend showed a regional association. And in this study, in situ and ex situ conservation approaches were raised for wild hawthorn protection utilization.

Genetic diversity and structure analysis of the endangered plant species Horsfieldia hainanensis Merr. in China

ABSTRACTThe genetic diversity and structure of nine natural populations of Horsfieldia hainanensis Merr., an endangered plant endemic to China, were studied using inter-simple sequence repeat markers. Nine primers were selected from 100 primers to evaluate 126 individual plants, from which a total of 136 bands were amplified and 108 bands were polymorphic. Our results demonstrated that the genetic diversity level of H. hainanensis was high with a percentage of polymorphic bands, Shannon's diversity index and Nei's genetic diversity index at the species level of 79.4%, 0.4787 and 0.3314, respectively, and correspondingly, averages of 40.4%, 0.2615 and 0.1843 at the population level. Significant genetic differentiation was observed among populations, showing that the coefficient of genetic differentiation among populations calculated using Nei's genetic diversity was 0.4509. The ranges of Nei's genetic identity and genetic distance among populations were 0.7387–0.8637 and 0.1466–0.3029, respectively. The unweighted pair group method with arithmetic mean clustering based on Nei's genetic distance indicated that nine natural H. hainanensis populations could be classified into two lineages. Collectively, we speculated that habitat fragmentation and disturbance from human activities could be considered the main reasons for the endangerment of H. hainanensis, and we propose in situ conservation for the existing natural H. hainanensis populations, especially at Mengtun, Niandou and Tongbiguan, where the genetic diversity is relatively high.

Development of genomic simple sequence repeat markers and genetic diversity analysis of Gracilariopsis lemaneiformis (Rhodophyta)

Gracilariopsis lemaneiformis is an economically important alga as it produces agar. Establishing a genetic breeding system for this species is crucial. Simple sequence repeat (SSR) markers have been used to establish such breeding systems in other species. In this study, abundant SSR loci were identified from the genome survey sequences of Gp. lemaneiformis, and their repeat numbers and lengths were determined. The repeat numbers of these SSRs ranged from 4 to 31, with 4 repeats being the most abundant number, representing 48.69%, while repeat numbers from 15 to 31 represented less than 1%. The total SSRs contained 120,873 bp, accounting for 0.12% of the genome, and the length of each SSR ranged from 12 to 62 bp, with an average of 15.62 bp. In 12 individuals, 120 SSRs were detected, 115 (95.83%) were successfully amplified, and 31 (25.83%) were developed into polymorphic primers. Subsequently, the polymorphic primers were used to screen 82 individuals from three geographical populations: Qingdao Sculpture Garden, Qingdao Zhanshan Bay, and Weihai Stone Island. Parameters, such as the observed number of alleles, effective number of alleles, Nei’s gene diversity index, Shannon’s diversity index, and polymorphism information content, indicated a low level of genetic diversity in the overall wild population. Genetic diversity was highest in the Weihai Stone Island population and lowest in the Qingdao Zhanshan Bay population. Based on Nei’s and Shannon’s diversity indices, the genetic variation within populations contributed the most to the total genetic variation, as indicated by the analysis of molecular variance. In addition, the genetic differentiation coefficient among populations was below 0.05, revealing that the degree of differentiation among the populations was low. A cluster analysis showed no obvious regional features, further indicating the non-significant differentiation among the three populations. These results suggest a scarcity of idioplasmic resources in Gp. lemaneiformis, which is related to its specialized living environment and reproductive mode. The over-exploitation of coastal areas is also an important factor affecting the low genetic diversity of the wild Gp. lemaneiformis population.

Demographic history and population genetic structure of Hagenia abyssinica (Rosaceae), a tropical tree endemic to the Ethiopian highlands and eastern African mountains

The distribution of genetic diversity among natural populations is significantly shaped by geographical and environmental heterogeneity. The key objectives of this study were to outline the population genetic structure and to investigate the effects of historical and current factors in shaping the population structure of an endemic tropical tree, Hagenia abyssinica. We used 11 polymorphic microsatellites to estimate genetic variability and evaluate gene flow among natural populations of H. abyssinica. Further, we employed ecological niche modeling approaches, to analyze the demographic history and map potential distributions of H. abyssinica during the Last Glacial Maximum and the present. Significant levels of genetic diversity (H O = 0.477, H E = 0.439) were observed among the sampled locations. High coefficient of genetic differentiation (F ST = 0.32) and considerable genetic variation within the sampled locations (68.01%) were detected. Our results indicated the existence of three genetic groups with limited gene exchange and revealed positive correlations (r = 0.425, P < 0.05) between genetic diversity and geo-graphic distance. The ecological niche modeling (ENM) results support the existence of three distribution zones during the Last Glacial Maximum (LGM), with high probability of occurrence (0.8–1.0), and indicated slight distribution disturbances during and after the LGM. The fundamental patterns of genetic diversity and population structuring of H. abyssinica result from a combination of both environmental and geographical factors, including long-term isolation by distance and characteristic life history of this species. Our ENM results identified three zones that could have served as glacial refugia for this species and lay a foundation for further studies, outlining demographic histories and population structures of Afromontane species.

Use of microsatellites for evaluation of genetic diversity in cherry tomato

Much of the diversity of tomato is found in wild forms, the most important being the Solanum lycopersicum L. var. cerasiforme and S. pimpinellifolium. The objective of this research was to assess the genetic diversity of 30 introductions of cherry tomato with 36 microsatellite molecular markers. The study was conducted at the Plant Transformation Research Center (PTRC) of the University of California. A dendrogram was built using the Dice-Nei and Li similarity index and the UPGMA clustering method, where introductions were differentiated without preserving a distribution pattern obeying the geographical area of origin. A coefficient of genetic differentiation was found (Fst = 0.3474), showing a high genetic differentiation of the introductions; those from Brazil, Ecuador, and Peru were the most genetically diverse, presenting 100% of polymorphic loci. The molecular variance analysis indicated a variation of 11% between the groups and 89% within the same. The broad genotypic variability of the evaluated introductions favors the possibility of selecting those for genetic improvement and sustainable use of the species.

English

Swertia chirayita is a highly valued but vulnerable medicinal plant species of Nepal. Its populations are declining in natural habitats due to over exploitation. Twenty-seven inter-simple sequence repeats (ISSR) primers were used to assess the genetic diversity and population genetic structure of 42 genotypes representing six natural populations of S. chirayita, from Nepal. Of the total 479 bands amplified by 27 ISSR primers, 473 (98.18%) were polymorphic, indicating very high level of genetic diversity at species level. Percentage polymorphism value for different primers ranged from 83.3 to 100% with an average of 98.18%. Polymorphism information content (PIC) value ranged from 0.88 to 0.93 with an average of 0.91. Cluster analysis performed with NTSYS pc statistical package using Jaccard&rsquo;s similarity coefficients generated from ISSR binary data matrix showed that, all 27 ISSR primers separated 42 individuals into two major clusters and six sub clusters at the similarity level of 0.24. The average value of Nei&rsquo;s genetic diversity (H) and Shannon&rsquo;s information index (I) equaled 0.276 and 0.423, respectively at species level. The coefficient of genetic differentiation (GST) amongst populations of S. chirayita was found to be high (0.548) with restricted gene flow (Nm=0.4829). Analysis of molecular variance showed that genetic diversity within populations is slightly higher (50.9%) than among populations (47.6%). The present genetic diversity assessment of S. chirayita populations has been of immense importance to understand the cause of its vulnerability and has furnished valuable insights for its conservation and sustainable utilization. &nbsp; Key words: Polymerase chain reaction, inter-simple sequence repeats (ISSR), genetic diversity, polymorphism, population genetics.

English

In this study, the genetic diversity and structure of 90 monosporidia mating-type isolates of Sporisorium scitamineum collected from China were comprehensively evaluated based on the DNA extracted from mating-type haploid sporidias using inter-simple sequence repeat (ISSR) polymorphism molecular marker technique. Fifteen selected ISSR primers produced 162 amplified DNA fragments, of which 115 (71.0%) were polymorphic. Polymorphic information content (PIC) values ranged from 0.12 to 0.92 with an average of 0.82, indicating that a moderate degree of genetic diversity exists among these 90 monosporidia mating-type isolates of S. scitamineum collected from China. Genetic differentiation coefficient (Gst) was calculated to be 0.320, indicating that the total genetic variation between populations was 32%, while 68% of the total genetic variation was from within populations. Meanwhile, gene flow (Nm) was 1.063, indicating lower rate of gene flow between populations. Based on the ISSR marker data set, the results of clustering by the unweighted pair group method of arithmetic average and principal component analysis were similar and could divide these 90 S. scitamineum isolates into two main groups. The isolates collected from the same province tend to cluster in the same main groups. This study shows that the genetic differentiation of these 90 monosporidia mating-type isolates of S. scitamineum was highly correlated with the ecological environment of collection sites, and the heterogeneity of ecological environment was the main driving force for the differentiation of S. scitamineum. &nbsp; Key words: Sugarcane, Sporisorium scitamineum, mating-type haploid sporidia, inter-simple sequence repeat, genetic diversity.

Effects of fragmentation and anthropic pressure on the genetic structure of Canthon (Peltecanthon) staigi (Coleoptera: Scarabaeidae) populations in the Atlantic Forest domain

Canthon (Peltecanthon) staigi is an endemic dung beetle from the east coast of South America (Brazil, Paraguay and Argentina). It is a stenotopic species abundant in different habitats of the Atlantic Forest. In this study, we analyzed the influence of fragmentation and environmental changes on the population genetic structure of C. (P.) staigi using inter-simple sequence repeat polymorphisms, and the consequences for management and conservation. The expected heterozygosity (HE) ranged from 0.16 (restinga, TAM population) in the smallest and most disturbed forest patch to 0.24 (“brejo de altitude”, PES population) in the largest and most conserved area. Based on the low coefficient of genetic population differentiation (FST = 0.07) and large molecular variance within populations, we suggest historical gene flow among C. (P.) staigi populations. Additionally, the model ƒ = 0, which corresponds to a lack of or very low inbreeding rate, is another factor that indicates gene flow among populations. Two genetic traits (K = 2) were related with anthropic disturbance, suggesting that the six studied populations are genetically divided into two separate units, one related to preserved and another to disturbed areas. Based on these data, the recent habitat fragmentation may not have led to genetic differentiation, but rather the environmental modifications caused by anthropic pressure seem to be strongly related to the loss of genetic diversity in the species C. (P.) staigi.

Adaptive genetic variability and differentiation of Croatian and Austrian Quercus robur L. populations at a drought prone field trial

Provenance trials, where populations of different geographical origin are tested in a common environment (common garden test), are a tool suited to allow the study of intraspecific adaptive genetic variation. Research of pedunculate oak (Quercus robur L.) adaptive genetic variability through analyses of populations in common garden tests has a long tradition. However, pedunculated oak populations originating south-eastern from the Alps have been scarcely studied in this way. This study addresses the adaptive genetic variability and differentiation of pedunculate oak populations originating from Austria and Croatia in a provenance/progeny field trial. Studied plants were six years old and were growing at the trial for three years. After two years of unusually low precipitations height and survival were analysed. The total mean height of all plants in the trial was 137.8 cm and ranged from 123.0 cm to 151.8 cm. The overall mean survival rate was rather high (0.85). Mean population survival ranged from 0.64 to 0.94. Individual narrow-sense heritabilities (hi2), family mean heritabilities (hf2), the coefficients of additive genetic variation (CVA) and quantitative genetic differentiation coefficients (QST) were calculated. A multivariate regression tree (MRT) analysis was used to determine the pattern of genetic differentiation of the populations. Individual heritabilities for height ranged between 0.00 and 0.39. Family mean heritabilities for height were rather low in most populations as well (<0.5). Family mean heritabilities for survival were higher than for height (ranging between 0.00 and 0.77). Calculated QST coefficients (0.25 for height and 0.14 for survival) indicated between-population genetic differentiation. The populations were separated into two clusters by MRT analysis regarding a climatic variable, namely Hargreaves’ reference evapotranspiration. Populations originating from comparatively more humid habitats were grouped in the first cluster. The first cluster had a lower mean height and survival compared to the second one. The differences between these clusters were highly statistically significant. The observed quantitative genetic differentiation might have been driven by natural selection caused by differences in the relative moisture of the habitats from which the progeny populations originate. The results suggest ecotypic pattern of the quantitative genetic differentiation among studied populations.

Genetic diversity of pine‐parasitic nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus in China

SummaryThe internal transcribed spacer (ITS) regions of rDNA have been routinely employed for identification and phylogenetic analysis of many nematode species. In this study, the intra‐ and interspecies ITS genetic diversity of Bursaphelenchus xylophilus and Bursaphelenchus mucronatus was evaluated. Ninety‐one isolates of the two nematode species collected from 14 Chinese provinces, Japan and Korea were used for ITS‐PCR and sequencing. An unweighted pair group cluster analysis dendrogram clustered them as two B. mucronatus and one B. xylophilus independent clades. Principal component analysis showed the phylogenetic relationship of the two nematode species more clearly; B. mucronatus isolates were separated into more than four groups, whereas B. xylophilus isolates still clustered into a group. The results of the Mantel test indicated the correlation of genetic distance matrices and geographic distance matrices was significant for both nematode species. The genetic differentiation coefficient (Gst) and gene flow (Nm) of B. mucronatus were 0.341 and 1.091, respectively, suggesting the importance of landscape heterogeneity and considerable obstacles for genetic exchange among B. mucronatus isolates in China. However, Gst and Nm of B. xylophilus were 0.188 and 2.151, respectively, very different compared to B. mucronatus. This could be owing to the short‐term introduction of B. xylophilus into China and a rapid spread through anthropogenic pathways. Our work adds to the understanding of the genetic diversity and genetic relationship of the two pine‐parasitic nematode species, and will aid in controlling them in the future.

Analysis on genetic diversity and genetic relationship of medicinal species in Coptis by SCoT

The genetic diversity and genetic relationship among four medicinal species of Coptis were detected by the approach of sequence-related amplified polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31. The systematic diagram of genetic relationship were clustered by TREECONW. The results showed that a total of 434 bands were produced by using 28 primers, of which 430 were polymorphic loci. There was a high level of genetic diversity among species (PPB=99.1%,Na=1.990 6,Ne=1.329 3,H=0.212 2,I=0.337 8). However, genetic diversity was lower within species, the average of genetic parameters wasPPB=16.8%,Na=1.168 2, Ne=1.073 0,H=0.043 7,I=0.067 7. The Nei's genetic differentiation coefficient was 0.794 0, that indicated that most of the genetic variation existed among species. By clustering analysis, different individuals gathered in the same group. The results confirmed that SCoT marker can be used as one of the effective methods to reveal the genetic diversity and relationship among medicinal species of Coptis.