Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps

This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33 %) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2–7 species.     

More polymorphic microsatellite markers in the European sea bass (Dicentrarchus labrax L.)

We provide details of five microsatellite loci screened in 163 individual sea bass. Large numbers of alleles were observed at three loci (20–25) and heterozygosities ranged from 0.52 to 0.86. These loci should prove useful for population genetic studies and for the pedigree analysis and genetic management of this species in aquaculture.     

Development of microsatellite markers in Dendrobium fimbriatum Hook, an endangered Chinese endemic herb

As an endangered endemic herb, Dendrobium fimbriatum, is under threat from numerous impacts. In order to analyse the genetic diversity and structure of this endangered species, we provide details of 10 microsatellite loci (out of 15 primer pairs designed) which showed polymorphic for D. fimbriatum. These loci were used to screen 25 individuals from across the species' geographical range. Ten loci were polymorphic with 2 to 19 alleles; three loci were monomorphic, while the rest produced no amplification fragments. These loci will be used to investigate population genetic structure, genetic diversity, conservation, and individual authentication in the endangered D. fimbriatum.     

DNA variants of the MHC show location-specific convergence between sheep, goat and cattle

Interspecific convergent evolution in sheep, goat and cattle was analysed with the help of orthologous microsatellite markers. Six of the loci are located in the major histocompatibility complex (MHC) region and three on different chromosomes. Samples from at least 60 animals per autochthonous breed of the three species were collected in central and southeast Anatolia (Turkey) as well as Baden-Württemberg (Germany). Allelic diversity, heterozygosity, population differentiation and genetic distances were calculated. The loci were polymorphic in all species and breeds. Apart from MSDRB, the loci linked to the MHC were similarly polymorphic as compared to the other loci. Allele numbers in the Turkish sheep and in the cattle breeds were higher than in the other breeds. The predominant occurrence of distinct allele lengths per locus differed depending on the species. For the three geographic locations, the genetic distances between species based on the MHC loci were significantly closer in comparison with distances based on quasi-neutral loci. This indicates convergent evolution of the MHC loci between sheep, goat and cattle caused by effects of location and demonstrates an approach for quantifying influences of adaptation on genetic variability.     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Comparison of genetic diversity at microsatellite loci and quantitative traits in hatchery populations of Japanese flounder Paralichthys olivaceus

Relationships of genetic diversity at microsatellite loci and quantitative traits were examined in hatchery-produced populations of Japanese flounder using a relatively straightforward experiment. Five hatchery populations produced by wild-caught and domesticated broodstocks were used to examine the effects of different levels (one to three generations) of domestication on the genetic characteristics of hatchery populations. Allelic richness at seven microsatellite loci in all hatchery populations was lower than that in a wild population. Genetic variation measured by allelic richness and heterozygosity tended to decrease with an increase in generations of domestication. In addition, the degree of genetic differentiation from a wild population increased with an increase in generations of domestication. Significant differences in three morphometric traits (dorsal and anal fin ray counts and vertebral counts) and three physiological traits (high temperature, salinity and formalin tolerance) were observed among the hatchery populations. The degree of phenotypic difference among populations was larger in morphometric traits than in physiological traits. The divergence pattern of some quantitative traits was similar to that observed at microsatellite loci, suggesting that domestication causes the decrease of genetic variation and the increase of genetic differentiation for some quantitative traits concomitantly with those for microsatellite loci. Significant positive correlation was observed between F _ST and the degree of phenotypic difference in the three morphometric traits and formalin tolerance, indicating that genetic variation at microsatellite loci predicts the degree of phenotypic divergence in some quantitative traits.     

用微卫星标记分析皱纹盘鲍群体的遗传变异

利用微卫星标记技术, 对皱纹盘鲍山东长岛和辽宁獐子岛的两个野生群体以及山东崆峒岛一个养殖群体的遗传变异进行了分析。对6个微卫星基因座的多态性进行了评估, 各基因座的多态信息含量(PIC)值均大于0.5, 适合对鲍群体遗传结构的分析。结果表明, 这6个基因座在3个皱纹盘鲍群体中共获得57个等位基因, 等位基因数(A)平均为9.50, 有效等位基因数(N_e)平均为5.8572, 平均杂合度观测值(H_o)和期望值(^H_e)分别为0.6925和0.7966; 两个野生群体的杂合度观测值(H_o)和期望值(H_e)均高于养殖群体。上述结果为保护和利用皱纹盘鲍的遗传多样性提供了依据。     

Genetic analysis of blood pressure in the Milan hypertensive strain of rat (Rattus norvegicus)

Estimates of heritability (h2) of blood pressure level and the number of loci controlling the trait were derived from two genetic crosses involving the Milan hypertensive strain of rat and its control with normal blood pressure. In the genetic cross involving backcrosses, the estimates were h2 = 64% and the number of loci was two or three; there was some evidence of dominance of the alleles for normal blood pressures. In the other cross with only F2's, the degree of genetic determination (heritability in the broad sense) was 45%, involving at least three loci.     

Isolation and characterization of microsatellite loci for parentage assessment in captive populations of roseate spoonbill (Ajaia ajaja)

Six microsatellite loci were isolated and characterized to assess genetic diversity and determine parentage in three captive roseate spoonbill (Ajaia ajaja) populations. Analysis of 61 individuals from three zoological parks and one wild population at five polymorphic loci revealed an average of six alleles per locus and expected heterozygosities from 59% to 81% (average 70%). Since spoonbills do not exhibit obvious sexual dimorphism, Aaju4, which exhibited ZW‐specific alleles, was exceptionally useful for sex identification. These loci will be valuable tools for investigating genetic diversity and documenting patterns of parentage in captive roseate spoonbill populations.     

Microsatellite DNA markers for Plasmopara viticola,the causal agent of downy mildew of grapes

Microsatellite loci were isolated from Plasmopara viticola (Oomycetes), the causal agent of downy mildew of grape, one of the most damaging fungal diseases of grapevine worldwide. Seven polymorphic loci were obtained from an enriched partial genomic library. A low genetic diversity was observed at all loci, with a mean observed allele number of 3.75 and an observed heterozygosity ranging from 0.074 to 0.547. Cross‐amplification tests on three closely related taxa indicated that two loci could be used in other Oomycetes species. These microsatellite loci were proved to be useful for population genetic analysis.     

Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci

Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.     

Development and characterization of microsatellite markers for Actaea racemosa (black cohosh, Ranunculaceae)

? Premise of the study: Microsatellite markers were developed in Actaea racemosa to analyze population genetic structure, compare genetic diversity across the species' range, and provide a genetic context for studies of phytochemical variation. ? Methods and Results: A total of seven polymorphic loci were screened in 60 individuals from 12 localities. The number of alleles per locus ranged from three to six, and observed heterozygosity ranged from 0.133 to 0.900. Most of the loci tested cross-amplified in A. pachypoda, A. podocarpa, and A. rubra, indicating the utility of these markers for the genus. ? Conclusions: These new loci will provide tools for population genetics studies, including the characterization of genetic variation in A. racemosa and other eastern North American species of Actaea.     

Microgeographic population genetic structure in the northern water snake, Nerodia sipedon sipedon detected using microsatellite DNA loci

We describe the isolation and genetic characterization of eight microsatellite DNA loci from the northern water snake, Nerodia sipedon sipedon and use these loci to analyse levels of genetic differentiation between local (< 2 km apart) populations of these snakes in Ontario. These loci are variable, with expected heterozygosities ranging from 0.28 to 0.91, and can correctly exclude nonsires in parentage analyses with a high probability (0.998). Population analyses reveal significant deviation from expected heterozygosity levels for one population, probably a result of a null allele(s) at a single locus and small but significant levels of genetic differentiation among all three populations. This demonstrates that microgeographic genetic structure exists in this species, possibly due to limited dispersal.     

Linkage disequilibrium between alleles at highly polymorphic mini- and micro-satellite loci of Theileria parva isolated from cattle in three regions of Kenya

Theileria parva schizont-infected lymphocyte culture isolates from western, central and coastal Kenya were analysed for size polymorphism at 30 T. parva-specific variable number tandem repeat (VNTR) loci using a panel of mini- and micro-satellite markers. The mean number of alleles ranged from 3 to 11 at individual loci and 183 distinct alleles were observed in total, indicating high genetic diversity within the T. parva gene pool in Kenyan cattle. The frequency distribution of the length variation of specific alleles among isolates ranged from normal to markedly discontinuous. Genetic relationships between isolates were analysed using standard indices of genetic distance. Genetic distances and dendrograms derived from these using neighbour-joining algorithms did not indicate significant clustering on a geographical basis. Analysis of molecular variance demonstrated that the genetic variation between individual isolates was 72%, but only 2.3% when isolates from different regions were pooled. Both these observations suggest minimal genetic sub-structuring relative to geographical origin. Linkage disequilibrium was observed between pairs of loci within populations, as in certain Ugandan T. parva populations. A novel observation was that disequilibrium was also detected between alleles at three individual pairs of VNTR loci when isolates from the three regional meta-populations were pooled for analysis.     

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

? Premise of the study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae). ? Methods and Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations. Eight loci amplified successfully and presented one to 10 alleles, and expected heterozygosities ranged from 0.097 to 0.862. Four loci also amplified in Pterodon emarginatus and presented similar polymorphism. ? Conclusion: The eight microsatellite primer pairs are potentially suitable for population genetic studies and successfully amplified in another Fabaceae species.     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans

The genetic variability at six cloned minisatellite loci was analyzed in minke whale populations from the North Atlantic, North Pacific, and Antarctic Oceans. Three loci displayed only a few different alleles in each of the three populations, with heterozygosity ranging from 0.00 to 0.47, and three loci revealed many different alleles in at least two fo the three populations, with heterozygosity ranging up to 0.98. Using small sample sizes, samples from two adjacent Antarctic Management Areas were not found to differ significantly in allele frequencies at any of the six loci. The use of principal coordinate analysis to detect multilocus disequilibria was explored. No significant evidence was found of intrapopulation heterogeneity within the pooled Antarctic sample. Pronounced interoceanic differences were observed at every locus, confirming the existence of genetic isolation found earlier using more conventional marker systems. The populations from the three oceans appear to have diverged to such a degree that the hypervariable loci have had time to evolve independently and arrive at different evolutionary stages in different populations. The frequency of undetected "null" alleles is remarkably high in minke whale populations compared to human populations and is probably a result of the cloning protocol used. Minisatellite loci are shown to provide a powerful population genetic tool, supplying levels of resolution appropriate to different degrees of evolutionary divergence.      

Mapping and Genetic Characterization of Loci Controlling the Restoration of Male Fertility in Ogura CMS Radish

Three Raphanus populations (BC1, F2 and R8) each segregating for the restoration of Ogura CMS were used tomap restorer loci. The three restorer loci, Rf1, Rf2 and Rf3, each exhibited dominant restoring alleles and wereeach mutually epistatic. Rf1 was mapped to the upper region of Rs1 using data from each population. Rf2 wasmapped to the middle of Rs2 using both the F2 and R8 populations. Rf3 was mapped to the upper region of Rs7using the R8 population. The marker analysis and linkage mapping of the BC1 and F2 populations were describedpreviously (Bett and Lydiate, 2003). Scoring at 114 marker loci in R8 population allowed a new map ofthe Raphanus genome to be integrated with the consensus map. The complex genetic control of the restoration ofOgura CMS in Raphanus is compared with the more simple genetic control of this trait previously described inB. napus. Markers linked to each of the three restorer loci will allow the routine generation and verification ofdefined restorer and maintainer lines for various combinations of defined restorer loci. Although the restorationof Ogura CMS in Raphanus probably involves additional loci, the identification of three loci and diagnosticmarkers for each provides a solid foundation for the development of a holistic model for the genetic control ofthis trait through mapping in additional populations.     

A genetic map of human chromosome 17p

A genetic linkage map was constructed with 18 loci from the short arm and pericentric region of chromosome 17 typed on the CEPH reference families. The genetic map includes three markers extracted from the CEPH public database. Nine loci could be ordered using a threshold of odds of at least 1000:1 against alternative orders during the map construction process. With a reduced tolerance of 100:1, a total of 13 loci could be placed on the map spanning a distance of approximately 60 cM in females and 46 cM in males. There were statistically significant differences between the male and the female genetic maps. The order inferred from the genetic data was consistent with the physical localizations of these probes obtained from somatic cell hybrids and tumor deletion studies. This map should be useful for genetic fine mapping of 17p loci.     

Relationship between heterozygosity and genetic distance in the three major races of man

In pairwise comparisons of gene frequency data from the three major races of man, the single locus measures of the heterozygosity within and the genetic distance between races are shown to be strongly correlated across the loci coding for red cell proteins and enzymes. The intercept of the regression line of genetic distance on heterozygosity in protein enzyme loci is statistically insignificant. These findings suggest that the genetic variability at the enzyme and protein loci in man is probably maintained by a balance of mutation and random genetic drift. At the blood group loci, however, the observed relationship between genetic distance and heterozygosity does not follow the expectation of the neutral mutation hypothesis. These observations are discussed in terms of the changes in probability of identical monomorphism in two populations during the process of gene differentiation.