Genetic differentiation and diversity analysis of medicinal tree Syzygium cumini (Myrtaceae) from ecologically different regions of India

This study represents the agro-ecological zone wise surveys of molecular variation of important medicinal tree Syzygium cumini Linn. (Jamun) which is native to India. It is used world wide in treatment of diabetes. Despite of its diverse medicinal properties no molecular data is available about the pattern of variation in its natural range. Populations of S. cumini in India are located in different habitats which differ from each other with regard to ecological factors. In this study, random amplified polymorphic DNA (RAPD) markers were used to detect inter and intra levels of genetic variations of sixteen S. cumini genotypes collected from three major agro-ecological zones of India. A total of 220 amplification products were scored of which 87.50 % were polymorphic. The level of polymorphism ranged from 47.69 % to 74.87 % polymorphic bands per population and was correlated with population size. Different measures of diversity: Shannon’s index of phenotypic diversity (I) = 0.451 ± 0.230; Nei’s genetic diversity (h) = 0.300 ± 0.172; effective number of alleles per locus (Ne) = 1.51 ± 0.347; total species diversity (Hsp) = 0.315 ± 0.031 and within population diversity (Hpop) = 0.158 ± 0.104 showed high genetic diversity at species level. Coefficient of genetic differentiation (Gst =0.498; Nm = 0.503) revealed significant genetic differentiation among the populations. Most of the genetic variations are contained among the populations. The results of cluster analysis and principal component analysis (PCA) give only little evidence for an ecotypic differentiation of S. cumini populations. Present genetic structure of population suggests ex situ conservation in seed banks in which seeds from at least five populations need to collected and conserved. Secondly, our study provides practical information to herbal drugs manufactures who use Jamun as a raw material.     

Genetic differentiation processes among the populations in India

The genetic variability in Indian populations is examined on the basis of the study of Tf, Gc, Gm, and Km polymorphisms. This variability is not associated with fluctuations, but is related to population history (mainly to migrations, hybrydization and caste endogamy). When genetic distances are calculated, Northern, Southern and Western Indian poplations show closer resemblances to Western Asian populations, while Eastern Indian populations are more similar to Mongoloid peoples.     

Genetic diversity in India and the inference of Eurasian population expansion

Background  

Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored.     

Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy–Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's F_ST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour‐joining phylogenetic trees based on D_A distances showed that the genetic relationships of present‐day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.     

Genetic diversity and differentiation of Siberian spruce populations at nuclear microsatellite loci

The results of the study of 21 populations of Siberian spruce (Picea obovata Ledeb.) from different parts of the species natural range by microsatellite (SSR) analysis of nuclear DNA are presented. Using nine loci developed for Picea abies (L.) Karst. and Picea glauca (Moench) Voss and detecting variation in Picea obovata, the parameters of intra- and interpopulation genetic diversity, as well as the degree of population differentiation, were determined. It was demonstrated that the population of Siberian spruce in the study was characterized by a relatively high average level of intrapopulation variability (H_o = 0.408; H_e = 0.423) and low interpopulation differentiation (F_st = 0.048, P = 0.001) at this class of DNA markers. The genetic distance between populations ranged from 0.009 to 0.167, averaging 0.039. The isolated Magadan population, located in the extreme Northeast of Russia at a considerable distance from the main species range and characterized by the lowest genetic diversity among the studied populations, was maximally differentiated from the rest of the spruce populations. In addition, the steppe Ubukun population from Buryatia and the population from the Bogd Khan Uul Biosphere Reserve, Mongolia, were considerably different in the genetic structure from most populations of Siberian spruce, although to a lesser extent than the Magadan population. These findings are consistent with the results of previous studies of this species carried out using allozyme and microsatellite loci of chloroplast DNA and point to the prospects of using nuclear microsatellites as DNA markers to analyze the population genetic structure of Siberian spruce.     

Genetic diversity within and genetic differentiation between blooms of a microalgal species

The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G.?semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.     

Genetic diversity and molecular differentiation of Chinese toad based on microsatellite markers

Genetic diversity and population structure of 9 populations of Bufo gargarizans with total 111 samples in China were assessed using seven microsatellite loci. The analysed microsatellite markers produced 161 alleles, varied from 9 to 38 alleles each locus. The number of alleles per population per locus ranged from 4.43 to 10.29. Polymorphic information content showed that all seven loci were highly informative (mean = 0.810 ± 0.071). The average observed heterozygosity was less than the expected (0.353 ± 0.051 and 0.828 ± 0.067, respectively). All tested populations gave significant departures from Hardy–Weinberg equilibrium. Genetic differentiation among the populations was considerably high with the overall and pairwise F _ST values (mean = 0.160 ± 0.039), and showed fairly high level of inbreeding (indicated by a mean F _IS value of 0.504 ± 0.051) and global heterozygote deficit. In comparison to other amphibian studies; however, our results suggested that the level of genetic structuring in B. gargarizans was relatively low in the geographical scale of the study area. Interestingly, the speculated population bottleneck was found to be absent and the analyses provide only weak evidence for a recent contraction in size even though there was severe inbreeding (indicated by the F _IS value) in the Chinese toad populations.     

Genetic differentiation and diversity of Acacia koa populations in the Hawaiian Islands

Acacia koa A. Gray (koa) is a leguminous tree endemic to the Hawaiian Islands and can be divided into morphologically distinguishable groups of A. koaia Hillebrand, A. koa and populations that are intermediate between these extremes. The objectives of this investigation were to distinguish among divergent groups of koa at molecular levels, and to determine genetic diversity within and among the groups. Phylogenetic analyses using the ITS/5.8S rDNA and trnK intron sequences did not separate the representative koa types into distinct clusters. An unweighted pair group method with arithmetic mean cluster analysis and principal coordinate analysis, based on allele profiles of 12 microsatellite loci for 215 individual koa samples, separated the population into three distinct clusters consistent with their morphology, A. koaia, A. koa and intermediate forms. There was an average of 8.8 alleles per polymorphic locus (AP) among all koa and koaia individuals. The intermediate populations had the highest genetic diversity (H′ = 1.599), AP (7.9) and total number of unique alleles (21), whereas A. koaia and A. koa showed similar levels of genetic diversity (H′ = 0.965 and 0.943, respectively). No correlation was observed between geographic distance and genetic distance as determined by a Mantel test (r = 0.027, P = 0.91). The data presented here support previous recommendations that morphological variation within koa should be recognized at the subspecific level rather than as distinct species.     

Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification

The genetic diversity and relationships amongst the dromedary (Camelus dromedarius) populations are poorly documented. Four recognized Kenyan dromedary breeds (Somali, Turkana, Rendille, Gabbra) and dromedary from Pakistan and the Arabian Peninsula (Saudi Arabia, United Arab Emirates) were studied using 14 microsatellite loci. Phylogenetic analysis showed that Kenyan dromedaries are distinct from Arabian and Pakistani populations. Expected heterozygosity and allelic diversity values indicate that Kenyan dromedaries are less diverse than non-Kenyan populations. With the exception of the Somali population, the Kenyan dromedaries are poorly differentiated (average FST=0.009), with only one to two loci separating the Gabbra, Rendille and Turkana populations studied (P < 0.05). Individual assignments were performed using the maximum likelihood method. A correct breed assignment of only 39-48% was observed for the Kenyan dromedaries, using an allocation stringency of a log of the odds ratio >2. Our results do not support the present classification of the indigenous Kenyan dromedary into four distinct breeds based on socio-geographical criteria. Instead, our results point to just two separate genetic entities, the Somali and a group including the Gabbra, Rendille and Turkana populations.     

入侵植物粗毛牛膝菊种群遗传多样性及遗传分化

利用ISSR分子标记技术,分析粗毛牛膝菊(Galinsoga quadriradiata)在中国分布的18个地理种群遗传多样性和遗传结构特点,为粗毛牛膝菊的防控奠定基础。结果表明:筛选的10条引物共扩增出349个位点,经Popgene软件分析,粗毛牛膝菊种群多态位点百分比(P)为8.88%~29.51%,Nei基因多样性指数(H)为0.0248~0.1023;种群遗传分化系数(Gst)为0.4663,种群间基因流(Nm)为0.5723;遗传相似度平均为0.9404,遗传距离平均为0.0621,UPGMA聚类分析将18个粗毛牛膝菊地理种群分为5大类;经Mantel检验,不同地理种群遗传距离与地理距离相关性不显著。研究表明,粗毛牛膝菊种群的遗传多样性较低;各地理种群间产生了一定程度的遗传分化;粗毛牛膝菊的入侵及扩散途径以人为多次反复传播为主。     

Genetic differentiation among some endogamous populations of Andhra Pradesh,India

Endogamous populations belonging to Brahmin, Vysya, Mala, and Madiga castes of Andhra Pradesh, South India, were investigated for certain red cell enzyme and serum protein genetic markers. Frequency values were statistically analyzed to assess genetic variation among the populations. Average heterozygosity of ten loci and genetic diversity within and between the populations were calculated by using the methods of Nei. Nei's index was used to calculate genetic distances between the pairs of populations. A dendrogram was drawn adapting the modified unweighted pair group method suggested by Li, which agreed with the history of the populations.     

Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis

Summary Genetic diversity and differentiation in indica and japonica groups of the cultivated rice (Oryza sativa L.) were studied by assaying DNA restriction fragment length polymorphisms of 12 indica and 14 japonica rice lines digested with three restriction endonucleases. A total of 49 probes were selected to represent the entire RFLP map at intervals of 20–30 cM. It was shown that 95 of the 145 possible probe/enzyme combinations, involving 43 probes and all three enzymes, detected restriction fragment length variation, and the degree of polymorphism varied greatly from one probe/enzyme combination to another. These results demonstrate that indica rice is genetically more diverse than japonica type. Significant differentiation between the two rice groups was detected by 33 probes representing 11 of the 12 rice chromosomes. It was deduced that the processes leading to differentiation involved a combination of molecular events that include base substitutions and insertion/deletions.     

Genetic diversity and differentiation of guanaco populations from Argentina inferred from microsatellite data

Genotype data from 14 microsatellite markers were used to assess the genetic diversity and differentiation of four guanaco populations from Argentine Patagonia. These animals were recently captured in the wild and maintained in semi-captivity for fibre production. Considerable genetic diversity in these populations was suggested by the finding of a total of 162 alleles, an average mean number of alleles per locus ranging from 6.50 to 8.19, and H(e) values ranging from 0.66 to 0.74. Assessment of population differentiation showed moderate but significant values of F(ST)=0.071 (P=0.000) and R(ST)=0.083 (P=0.000). An amova test showed that the genetic variation among populations was 5.6% while within populations it was 94.4%. A number of 6.6 migrants per generation may support these results. Unambiguous individual assignment to original populations was obtained for the Pilcaniyeu, Las Heras and La Esperanza populations. The erroneous assignment of 18.75% Rio Mayo individuals to the Las Heras population can be explained by the low genetic differentiation found between these two populations. Thirty-nine of 56 loci per population combinations were in Hardy--Weinberg disequilibrium because of guanaco heterozygote deficiency, which may be explained by population subdivision. The high level of genetic diversity of the guanacos analysed here indicates that the Patagonian guanaco constitutes an important genetic resource for conservation or economic utilization programmes.     

Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers

To determine genetic diversity and evolutionary relationships among Chinese buffalo populations, 18 indigenous swamp buffalo populations and two introduced river buffalo breeds were genotyped for 30 microsatellite loci. The mean number of alleles across the 30 loci was 8.13, and the expected heterozygosity ranged from 0.517 (Yanjin) to 0.609 (Dehong). Although there was abundant genetic variation, genetic differentiation between Chinese buffalo populations was low, with only 2.8% of the total genetic variance among populations. The genetic differentiation pattern and genetic relationships among Chinese buffalo populations were consistent with their geographic distribution. The Dehong population was discerned as a distinct indigenous population, but suffered genetic admixture with river buffalo. The remaining populations were divided into four major clusters, i.e. the Upper and Middle Reaches of Yangtze Valley cluster (Guizhou, Guizhoubai, Yanjin, Fuling, Enshi and Jianghan), the Lower Reaches of Yangtze Valley cluster (Haizi, Shanqu and Dongliu), the South China cluster (Fuan and Xinfeng) and the Southwest China cluster (Xinglong, Xilin, Diandongnan and Dechang).     

Genetic diversity and genetic differentiation in Daphnia metapopulations with subpopulations of known age

If colonization of empty habitat patches causes genetic bottlenecks, freshly founded, young populations should be genetically less diverse than older ones that may have experienced successive rounds of immigration. This can be studied in metapopulations with subpopulations of known age. We studied allozyme variation in metapopulations of two species of water fleas (Daphnia) in the skerry archipelago of southern Finland. These populations have been monitored since 1982. Screening 49 populations of D. longispina and 77 populations of D. magna, separated by distances of 1.5-2180 m, we found that local genetic diversity increased with population age whereas pairwise differentiation among pools decreased with population age. These patterns persisted even after controlling for several potentially confounding ecological variables, indicating that extinction and recolonization dynamics decrease local genetic diversity and increase genetic differentiation in these metapopulations by causing genetic bottlenecks during colonization. We suggest that the effect of these bottlenecks may be twofold, namely decreasing genetic diversity by random sampling and leading to population-wide inbreeding. Subsequent immigration then may not only introduce new genetic material, but also lead to the production of noninbred hybrids, selection for which may cause immigrant alleles to increase in frequency, thus leading to increased genetic diversity in older populations.     

Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers

Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.     

Genetic diversity and differentiation of populations of scots pine in Southern Siberia and Mongolia

This paper presents the results of studying the genetic diversity, structure, and degree of differentiation of island populations of Scots pine (Pinus sylvestris L.) growing in Southern Siberia (south of Krasnoyarsk krai, Khakassia, Tuva, and Buryatia) in the northeastern part of Mongolia, which were obtained on the basis of an analysis of 20 isoenzymic loci.     

Genetic diversity and differentiation of the extremely dwarf Ficus tikoua in Southwestern China

Fig wasps are short-lived, weak fliers, and their long-distance dispersal depends on the ability to enter fast-flowing air above the canopy. Therefore, growth form of fig species may affect fig wasps’ dispersal. We employed six microsatellite markers to examine gene flow in Chinese populations of the dioecious Ficus tikoua, a prostrate shrub with figs partially buried in the soil. Moderate genetic diversity was found within populations of F. tikoua. Differentiation among six F. tikoua populations (F_ST = 0.196, p < 0.001) was higher than those of other dioecious figs, and significant differentiation was found between each pair of populations, indicating potential restricted gene flow. This was further demonstrated by significant isolation-by-distance pattern (p = 0.039), because low gene flow among population was needed to balance the minor effect of genetic drift, given F. tikoua was locally common. Restricted gene flow suggests that growth form may determine differences in gene flow between fig species.