Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting

We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance.     

SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India

Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes.     

Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae) (oat)

? Premise of the study: A new set of microsatellite primers was developed for Avena sativa and characterized to assess the level of genetic diversity among cultivars and wild genotypes. ? Methods and Results: Using an enrichment genomic library, 14 simple sequence repeat markers were identified. The loci of these markers were characterized and found to be polymorphic in size among 48 genotypes of oat from diverse geographical locations. The number of alleles per locus ranged from two to eight, while the observed heterozygosity ranged from 0.031 to 0.75. ? Conclusions: These newly identified microsatellite markers will facilitate genetic diversity studies, fingerprinting, and genetic mapping of oat. Moreover, these new primers for A. sativa will aid future studies of polyploidy and hybridization in other species in this genus.     

Genetic Diversity of Kenaf (Hibiscus cannabinus) Evaluated by Inter-Simple Sequence Repeat (ISSR)

Understanding genetic diversity is very useful for scientific utilization for breeding. In this study, we estimated the genetic distances in a panel of 84 kenaf accessions collected from 26 countries and regions using ISSR markers. The results of UPGMA analysis showed that kenaf germplasm had abundant genetic variation, with genetic dissimilarity coefficients ranging from 0.01 to 0.62. The in-group dissimilarity coefficient (0.29) was observed in 84 kenaf accessions, and all the accessions could be divided into three groups: cultivars (L_1–1), relatively wild species (L_1–2 and L_1–3), and wild species (the others). Further in-group analysis in group L_1–1 (0.19) revealed that the kenaf cultivars could be divided into five subgroups with distinct regional characteristics. It is imperative that genes be exchanged among all kinds of tested varieties from different origins. The results provide a useful basis for kenaf germplasm research and breeding.     

Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR)

Twenty seven accessions of sorghum conserved in the national gene bank of Zambia, representing two of the three agroecological regions of the country, were investigated using simple sequence repeats (SSR) markers in order to determine the extent and distribution of its genetic diversity. We used 10 microsatellite primer-pairs, which generated 2-9 alleles per locus and a total of 44 alleles across the 27 accessions. The observed heterozygosity (Ho(P) ) among the accessions ranged from 0 to 0.19 with an average of 0.04 whereas the average expected heterozygosity (He(P) ) among accessions was 0.07 in line with the fact that sorghum is predominately inbreeder. The analysis of molecular variance (AMOVA) revealed that 82% of the total genetic variation was attributable to the genetic variation among accessions (F(ST) = 0.824; p < 0.001) whereas the genetic variation within accessions accounted for 18% of the total genetic variation. AMOVA on sorghum accessions grouped based on four ethnic groups (Soli, Chikunda, Lozi and Tonga) associated with collection sites revealed a highly significant variation among groups (23%; p < 0.001). Although cluster analysis grouped most accessions according to their sites of collection, some accessions that originated from the same site were placed under different clusters. In addition to the extent and pattern of genetic diversity, consideration should also be given to other factors such as ecogeographic and ethnic differences when sampling sorghum genetic resources for rational and efficient conservation and utilization in the breeding program.     

Postglacial colonisation of western Central Europe by Polyommatus coridon (Poda 1761) (Lepidoptera: Lycaenidae): evidence from population genetics

The genetic population structure of Polyommatus coridon (Poda 1761) over large regions of France, Italy and Germany was studied by allozyme electrophoresis. The genetic diversity within populations was high for all parameters analysed (number of alleles 2.72; observed and expected heterozygosity 19.6% and 20.3%, respectively; percentage of polymorphic loci: total: 76.4% and, with polymorphism if the frequency of the commonest allele is below 95%: 53.1%), whereas genetic differentiation between populations was comparatively low (FST = 0.021 +/- 0.002). The mean number of alleles declined significantly from southern to northern populations (r = -0.53, P = 0.0005). Similar effects were found also for other parameters of genetic diversity. This is interpreted as a loss of genetic diversity during postglacial expansion. However, samples from France and Italy had similar patterns of genetic diversity indicating no significant loss in this region. Populations from southern Germany were genetically uniform, well differentiated from French populations and showed a significant loss of genetic diversity. Probably, this is due to a bottleneck during passing through the Burgundian Gap, which is a migration corridor from north-eastern France to southern Germany. In contrast to southern German populations, western German populations were not well differentiated from French populations. Nevertheless, they were genetically impoverished, probably as a result from local bottlenecks and post-expansion phenomena.     

Allozyme diversity in natural populations of Viola palmensis Webb & Berth. (Violaceae) from La Palma (Canary Islands): implications for conservation genetics

Genetic diversity was measured by allozyme electrophoresis in eight natural populations of the threatened Canarian endemic Viola palmensis Webb & Berth. (Violaceae). Nineteen alleles corresponding to 11 gene loci were detected. High levels of genetic diversity were found, ranging from 36.3 to 45.4 % for the percentage of polymorphic loci (P), from 1.45 to 1.60 for the average number of alleles per locus (A) and from 0.128 to 0.200 for the expected heterozygosity (H(e)). Between 85.5 and 96.6 % of genetic variability was apportioned within populations. As a whole, populations were not at Hardy-Weinberg equilibrium, with a deficit of heterozygous individuals attributable to the existence of genetic structuring in the populations analysed. The levels of interpopulation genetic differentiation were low (mean F(ST) = 0.100), while genetic identity pair-wise comparisons were high (mean I = 0.973) suggesting considerable levels of gene flow among populations. No relationship was detected between genetic differentiation and geographical distances between populations. An outcrossing insect-mediated breeding system might contribute to pollen dispersion of this species. For conservation genetics we suggest in situ preservation areas are defined that are free of disturbance and that include populations with the highest genetic diversity.     

Study of transferrin (TF), group specific component (GC) and alpha-1-antitrypsin (PI) subtypes in the populations of Basque country (Spain)

Genetic polymorphisms of three serum proteins Transferrin (TF), Group Specific Component (GC), and Alpha-l-Antitrypsin were investigated by isoelectric focusing (IEF) in the Basque and non Basque populations from Vizcaya and Guipuzcoa, Spain. Two of the three genetic systems (TF and PI) showed conclusive genetic heterogeneity between the Basque populations of these two provinces. In addition to the past genetic drift, the present day genetic differentiation in the Basque country seems to be contributed by the unique structure of its populations.     

Exploring the assumptions underlying genetic variation in host nematode resistance (Open Access publication)

The wide range of genetic parameter estimates for production traits and nematode resistance in sheep obtained from field studies gives rise to much speculation. Using a mathematical model describing host – parasite interactions in a genetically heterogeneous lamb population, we investigated the consequence of: (i) genetic relationships between underlying growth and immunological traits on estimated genetic parameters for performance and nematode resistance, and (ii) alterations in resource allocation on these parameter estimates. Altering genetic correlations between underlying growth and immunological traits had large impacts on estimated genetic parameters for production and resistance traits. Extreme parameter values observed from field studies could only be reproduced by assuming genetic relationships between the underlying input traits. Altering preferences in the resource allocation had less pronounced effects on the genetic parameters for the same traits. Effects were stronger when allocation shifted towards growth, in which case worm burden and faecal egg counts increased and genetic correlations between these resistance traits and body weight became stronger. Our study has implications for the biological interpretation of field data, and for the prediction of selection response from breeding for nematode resistance. It demonstrates the profound impact that moderate levels of pleiotropy and linkage may have on observed genetic parameters, and hence on outcomes of selection for nematode resistance.     

GENETIC VARIABILITY OF GELIDIUM CANARIENSIS (RHODOPHYTA) DETERMINED BY ISOZYME ELECTROPHORESIS1

The populations of Gelidium canariensis (Grunow) Seoane-Camba from the Canary Islands were analyzed for genetic variability by isozyme electrophoresis in 1989 and 1990. Each population was divided into sporophytic and gametophytic subpopulations. Twenty-three to 27 putative alleles corresponding to 22 gene loci were analyzed. Sev-enteen loci were monomorphic in all six subpopulations, and five were polymorphic in at least one subpopulation. Significant deviations from Hardy-Weinberg equilibrium were found. The amount of genetic variability (percentage of polymorphic loci, mean number of alleles per locus, and average gene diversity) of haploid subpopulations was lower than that of diploid subpopulations. No correlation between genetic distance and geographical distance was found. Low genetic differentiation between sporophytic and gametophytic subpopulations of the same locality was obsewed in two populations. The low genetic diversity and genetic differentiation suggest that the genetic structure of the populations of G. canariensis from the Canary Islands is due to a combination of founder effects and the predominance of asexual reproduction. Initial differences in gene frequencies may have persisted because of insufficient time to reach a higher level of differentiation.     

Microsatellite markers for Lycium ruthenicum (Solananeae)

We developed microsatellite markers in Lycium ruthenicum, a desert plant widely distributed in northwestern China. In order to investigate its population genetic structure, genetic diversity, and its evolutionary history, we have isolated 11 novel microsatellite loci primers and characterized them in 24 individuals from 3 populations of L. ruthenicum using the combined biotin capture technique. For these microsatellites, one to seven alleles per locus were identified. The observed heterozygosities ranged from 0 to 0.958, meanwhile the expected heterozygosities ranged from 0 to 0.841. These microsatellite markers could be first useful for population level studies like genetic diversity and structure in this species.     

Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi

White-tailed deer (Odocoileus virginianus) were nearly extirpated from the southeastern USA during the late 19th and early 20th centuries. Recovery programmes, including protection of remnant native stocks and transplants from other parts of the species' range, were initiated in the early 1900's. The recovery programmes were highly successful and deer are presently numerous and continuously distributed throughout the southeastern USA. However, the impact of the recovery programmes on the present genetic structure of white-tailed deer remains to be thoroughly investigated. We used 17 microsatellite DNA loci to assess genetic differentiation and diversity for 543 white-tailed deer representing 16 populations in Mississippi and three extra-state reference populations. There was significant genetic differentiation among all populations and the majority of genetic variation (> or = 93%) was contained within populations. Patterns of genetic structure, genetic similarity and isolation by distance within Mississippi were not concordant with geographical proximity of populations or subspecies delineations. We detected evidence of past genetic bottlenecks in nine of the 19 populations examined. However, despite experiencing genetic bottlenecks or founder events, allelic diversity and heterozygosity were uniformly high in all populations. These exceeded reported values for other cervid species that experienced similar population declines within the past century. The recovery programme was successful in that deer were restored to their former range while maintaining high and uniform genetic variability. Our results seem to confirm the importance of rapid population expansion and habitat continuity in retaining genetic variation in restored populations. However, the use of diverse transplant stocks and the varied demographic histories of populations resulted in fine-scale genetic structuring.     

Genetic profile of alloxan-induced diabetes-susceptible mice (ALS) and-resistant mice (ALR)

Two inbred strains from a foundation stock derived from Crj: CD-1 (ICR) mice were established after more than 20 generations of full-sib mating, and by simultaneous selective breeding for developing and not developing diabetes after alloxan administration (45 mg/kg in males, 47 mg/kg in females). To elucidate the genetic background of the two inbred strains, i. e., alloxan-induced diabetes-susceptible (ALS) strain and alloxan-induced diabetes-resistant (ALR) strain, their biochemical genetic markers and immunogenetic markers were examined. 1) For both strains, investigation of biochemical genetic markers at 19 loci and immunogenetic markers at 11 loci revealed no variation in any gene within the same strain, showing to be homogeneous, thus indicating establishment of the inbred strains. 2) The two strains differed from each other at 2 loci of biochemical genetic markers and at 5 loci of immunogenetic markers. 3) The ALS and ALR strains can be regarded as new inbred strains derived from ICR mice. 4) The results show that the marker genes of the two strains are different at 7 loci, but it remains unclear whether or not these genes are involved in the difference between the two strains in susceptibility to alloxan.     

Quantitative genetic diversity and conservation strategies for an allogamous annual species,Dasypyrum villosum (L.) Candargy (Poaceae)

Dasypyrum villosum (L.) Candargy is a weedy annual diploid (2n = 14, VV genomes) allogamous grass species (Poaceae, Triticeae). Genetic variation for 12 traits was studied in 43 natural populations (31 from Italy and 12 from Croatia and Montenegro of former Yugoslavia) grown in a common field environment in California. Although 7 of 12 traits followed the theoretical prediction that a larger proportion of genetic variation was distributed within populations than among populations, exceptions were found for spike length, plant height, and days to flag-leaf emergence, heading, and anthesis. Covariate analysis showed that developmentally closely related characters were more likely correlated at both population and family within population levels. Geographically closer populations shared more genetic similarity than distant populations as indicated by mean coefficients of variation and cluster analysis of the Euclidean distances among populations. As few as five populations, each population with five or more half-sib seeds taken randomly from 5 plants, is expected to capture more than 95% of the total genetic variation of this species in the region sampled, but sampling a much larger number of seeds per population (> 1000) for long-term storage would supply research and plant breeding needs for several decades. If seed regeneration is required, populations can be sampled from clusters having similar genetic variation, and grown in reproductive isolation or bulked seed samples from all populations of each cluster group can be grown in isolation. The former is recommended if population integrity is desired while the latter is sufficient to provide genetic resources for plant-breeding purposes.     

Genetic Diversity and Population Structure Analyses of Wild Relatives and Cultivated Cowpea (Vigna unguiculata (L.) Walp.) from Senegal Using Simple Sequence Repeat Markers

Cowpea (Vigna unguiculata (L.)) is an important crop for food security in Senegal; therefore, understanding the genetic diversity of local germplasm is relevant for crop improvement and genetic maintenance in the era of climate change. For this purpose, 15 microsatellite markers were used to estimate the genetic diversity of Senegalese cowpea germplasm, including 671 accessions grown in eight regions and 66 wild relatives and intermediate forms (weedy). For the cultivated, the main expected heterozygosity (mHe) ranged between 0.317 (Fatick) and 0.439 (South). A narrow genetic variation between accessions from the different regions was observed with genetic similarity ranging from 0.861 to 0.965 and genetic differentiation indices (Fst) between 0.018 and 0.100. The accessions from southern Senegal (Kédougou, Sédhiou, and Kolda regions) are more diverse than the others. However, the accessions from the North (Saint-Louis) are genetically different from other regions. The diversity analysis in wild relatives from Senegal, which had never been performed before, revealed that the wild/weedy forms remain more diverse than the cultivated with genetic diversity values (He) of 0.389 and 0.480, respectively. STRUCTURE software divided the Senegalese germplasm into five subpopulations. Three of them (i, ii, and iii) included only cultivated accessions from several regions, one (v) mainly from Saint-Louis, and one (iv) the wild/weedy with some cultivated accessions. Our results support the hypothesis that Vigna unguiculata var. spontanea is the wild progenitor of cowpea. The accessions from the South, the northern recession accessions, and the wild/weedy could serve as sources of new genes for the genetic improvement of cowpea in Senegal.

     

Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis)

Ten novel microsatellite loci were isolated from giant scallop Mizuhopecten yessoensis, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from two to 17, and the observed and expected heterozygosities ranged from 0.17 to 0.99 and 0.33 to 0.90, respectively. Six loci showed significant Hardy–Weinberg disequilibrium. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.     

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next‐generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower.     

Development of intron targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae)

? Premise of the study: Intron Targeting (IT) primers were developed for potato using expressed sequence tags (EST) and NCBI database records to study genetic diversity. ? Methods and Results: Twenty-nine polymorphic intron targeting (IT) markers were generated and characterized from 30 samples of potato and 22 samples of Solanum nigrum to detect polymorphism. The number of alleles (A) per locus ranged from 2 to 7 in the analyzed populations, and the observed heterozygosity (H(O)) and expected heterozygosity (H(E)) from 0 to 0.833 and 0.750, respectively. All of the primers also amplified in the related species S. nigrum. ? Conclusions: The developed markers will provide valuable tools for genetic diversity analysis, genetic mapping, and marker-assisted breeding of potato and related Solanum species.     

圈养小熊猫遗传多样性与种群遗传结构分析

小熊猫是亚洲特有的珍稀濒危动物,目前受到栖息地减少、片断化和人类活动干扰等威胁。中国圈养小熊猫已经有60 多年历史,约55 个机构曾经饲养过小熊猫,现今圈养数量有400 多只,评估小熊猫圈养种群的遗传多样性和遗传结构对科学维持圈养种群和保存遗传种质资源意义重大。本研究利用19 个微卫星座位,对中国境内11 个小熊猫圈养种群的116 只个体进行了遗传多样性评估及遗传结构分析。结果显示11 个种群都具有较高的遗传多样性,平均基因丰富度3.505 ± 1.033 (北京)至4.026 ± 1.219 (冕宁),期望杂合度0.631 ± 0.225(黄山)至0.782 ±0.171 (温岭)。其中福州和无锡种群极显著偏离Hardy-Weinberg 平衡。整个圈养群体内各个种群遗传分化系数为0.055,呈显著分化,表明11 个种群遗传分化水平较高。Bayesian 遗传聚类分析将11 个种群聚为三个遗传簇,与野生种群的遗传聚类结果一致。结论:小熊猫圈养种群与野生种群相比,同样具有较高的遗传多样性。因此,圈养小熊猫遗传管理的重点不再是引进野生个体充实圈养种群,应制订科学的繁殖计划,避免近交,从而维持圈养种群的遗传多样性。     

Genetic diversity and population structure of Elytrigia pycnantha (Godr.) (Triticeae) in Mont Saint-Michel Bay using microsatellite markers

During the last decade, an invasive wheatgrass species (Elytrigia pycnantha) has colonized the low salt marshes of the Mont Saint Michel Bay resulting in an accelerated change in the vegetation. This study was conducted using microgeographical genetic diversity in order to understand the genetic structure of this invasive and clonal species. Genetic variation and population structure of fifteen populations collected in high and low marsh habitats around the Bay were analyzed using five microsatellite loci. Because E. pycnantha is an allohexaploid, the application of standard genetic diversity statistics was not possible; we chose to summarize genetic diversity using statistics calculated from banding phenotypes. The mean number of alleles per locus was 10.2, the mean number of different alleles per sample was 6.87. The mean number of allelic phenotypes across all populations was 7.21. The mean value of genetic diversity for the species, calculated as the average number of alleles by which pairs of individuals differ, was H's = 1.91 and H't = 2.04. Little genetic differentiation among populations was detected (0.067). The association between pairwise genetic differentiation and geographic distances exhibited no evidence for isolation by distance. A geographical pattern of population differentiation, where a single population GI was clearly separated from the remaining population groups (considered as a metapopulation), was revealed by principal component analysis (PCA), and we propose that this is because GI represents a new genotype.