Polymorphic Microsatellite DNA Research Articles

Genetic Characterizations of the Iranian Honey Bee (Apis mellifera meda Skorikov 1929) Populations Using the Microsatellite DNA Markers.

The genetic characterization of the Iranian honey bee was investigated by analyzing 10 polymorphic DNA microsatellite loci in 300 honey bee samples representative of twenty Iranian provinces. This study evaluated the heterozygosity (Ho and He), the Shannon index, the number of observed alleles, and F-statistics among tested populations as genetic parameters. Our finding demonstrated that the Iranian honey bee populations were described by low genetic diversity in terms of the number of observed alleles, Shannon index, and Heterozygosity values. Most populations had significant deviations from Hardy Weinberg equilibrium cause of heterozygote shortage. Low FST and FIS values proposed the absence or very low genetic diversity within and among A. m. meda populations in the present study. The cluster analysis has categorized the honey bee samples gathered from various regions of Iran into two main groups, including honey bees in the North-West (i.e., North, Northwest, and West) provinces and honey bees in the East-South (i.e., Eastern North, Central part, and Southern) provinces of Iran. Our results also revealed lower genetic differentiation and heterozygosity among tested honey bee populations. The results from this study are consistent with previous investigations in Iran, alarming the loss of genetic diversity in the Iranian honey bee populations, which leads to more homozygosity. This study presented new data and reports on genetic structure in investigated native Iranian honey bee populations, and it will benefit future studies on selection, native biodiversity preservation and other conservation breeding projects.

Genetic Structure of Apis cerana Populations from South Korea, Vietnam and the Russian Far East Based on Microsatellite and Mitochondrial DNA Polymorphism.

In this article, we present the results of the genetic analysis of Apis cerana samples from the Russian Far East, South Korea and Vietnam. An analysis of the polymorphism of seven microsatellite loci and an assessment of the haplotype diversity of the mtDNA tRNAleu-COII locus were performed. A fragment of about 431 bp in tRNAleu-COII was sequenced. The analysis showed the presence of 14 haplotypes, while the predominant haplotype was Japan1. Microsatellite data revealed two differentiated clusters. The first cluster contained tropical climate A. cerana samples from Vietnam, and the second cluster combined temperate climate A. cerana samples from the Russian Far East and South Korea.

Multiple mating by both sexes in an invasive insect species, Aethina tumida (Coleoptera: Nitidulidae).

Multiple mating by both sexes is common among sexually reproducing animals. Small hive beetles (SHB), Aethina tumida, are parasites of bee nests endemic to sub-Saharan Africa and have become a widespread invasive species. Despite the considerable economic damages they can cause, their basic biology remains poorly understood. Here we show that male and female small hive beetles can mate multiple times, suggesting that costs for mating are low in this species. In an invasive A. tumida population in the United States, a combination of laboratory experiments for males and paternity analysis with eight polymorphic DNA microsatellite markers for field-caught females were used to estimate the number of mating by both sexes. The data show that females and males can mate multiple times-females mated with up to eight males, whereas males mated with at least seven females. The results also showed that A.tumida displayed a skewed paternity, although this was not consistent among the tested females. Thus, first or last male advantage seem to be unlikely in A.tumida. Our observations that individuals of both sexes of A. tumida can mate multiple times opens new research avenues for examining drivers of multiple mating and determining the role it may play in promoting biological invasions.

Genetic relationships among emu populations in Japanese farms based on mitochondrial and microsatellite DNA polymorphisms.

Emus (Dromaius novaehollandiae) are expected to become a novel poultry species for producing eggs, meat, and oil. In our previous studies, Japanese emu populations were predicted to have reduced genetic diversity through inbreeding. For a sustainable emu industry in Japan, it is necessary to understand the current genetic structure and relationships in dispersed farms. In this study, we investigated the genetic structure and relationships of six Japanese emu farms based on mitochondrial DNA and microsatellite polymorphisms. We analyzed the DNA sequences of the mitochondrial D-loop region in 157 individuals and detected four haplotypes with four nucleotide substitution sites (Hap-a, Hap-b, Hap-c, and Hap-d). Analysis of molecular variance revealed that 43.6% of total variance was "among population," and the FST value was 0.436 with significant genetic differentiation (P < 0.001). In microsatellite analysis, the expected (HE ) and observed (HO ) heterozygosities were 0.53-0.64 and 0.44-0.59, respectively. Phylogenetic trees and STRUCTURE analysis revealed that the six Japanese farmed emu populations could be divided into four genetically differentiated groups. Therefore, we identified genetic resources that may be useful in extending the genetic diversity of Japanese farms and are predicted to contribute to the conservation and reconstruction of populations.

Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish.

Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.

Microsatellite DNA Polymorphism Studies in Mudhol Hound Dog Native of India

Background: Mudhol Hound the popular dog breed of Karnataka State, India has a long historical association with wars, hunting, social bondage, guarding and recently with the Indian army as a part of army’s sniffer dog squad. Despite its unique qualities, the number of animals is getting reduced gradually. Hence the present study was aimed at molecular characterization of the Mudhol Hound which will be useful in maintenance of diversity of the breed. Methods: In this study, 26 microsatellite markers were used for the characterization of Mudhol Hound dog. A total of 50 blood samples were screened. Microsatellite loci were analyzed by running the PCR products on 6.5 per cent polyacrylamide gels followed by silver staining. Genotyping was done based on the banding patterns. Result: A total of 221 alleles were observed from the 26 microsatellites. The number of alleles ranged from 5 (AHTk211) to 12 (INU055, PEZ12) with a mean of 8.5±1.9442 alleles. The average H0 and He were 0.7685±0.2122 and 0.8326±0.0397, respectively. The percentage of polymorphic loci obtained was 100 as all the loci studied were found to be polymorphic having the PIC values more than 0.5. All the 26 loci showed significant deviation from Hardy - Weinberg equilibrium (P less than 0.001).

GENETIC RELATIONSHIPS BETWEEN NATIVE SHEEP BREEDS IN NIGERIA BASED ON MICROSATELLITE DNA POLYMORPHISMS.

Genetic relationship among Nigeria's breeds of sheeps and crosses was studied using microsatellite DNA polymorphisms. DNA samples extracted from four Nigeria's breeds of sheeps (West African Dwarf,the balami, Uda and yankassa) and crosses were analysed using 30 microsatellite markers for diversity studies. Twenty of the makers were by the sheeps genome . Nineteen of the loci were polymorphic and were used to calculate genetic distances (Ds) between the based on allelefrequences of microsatellite. The phylogenetic relatioship between the breeds were similarly estimated. With the total number of loci studied, 285 alleles were generated and a high decree of heterozysity was recorded, (0.57 to 0.72), a relative high degree of relaibility could be placed on the tree topology with the relationship between breeds potraying a closer relationship between the yankassa and Uda (Ds 0.356). The genetic distance (Ds) was 0.432, 0.534 and 0.665 between the African Dwarf and the Yankassa, Uda and Balami respectively also indictating a closer relatioship between the Yankassa, and the WAD compared to the basically Northern breeds (Uda and Balami). This further confirms the evolutionary divergence of the breeds which makes them distint entitles. The data suggests that microsatellite DNA markers are useful tools for studying the genetic relationship among these sheeps breeds. The high polymorphic alleles could thus be exploited in breeds improvement and development.

Полиморфизм ДНК собак (Canis familiaris L.). III. VNTR- и STR-локусы. Их применение в собаководстве и криминалистике

The application of mini- and microsatellite polymorphisms of dog DNA, also referred to as VNTR- and STR-loci, respectively, in dog breeding and criminalistics is considered. Their use in dog breeding is shown to clarify pedigrees, establish paternity and purebred, as well as to differentiate breeds mainly in the form of microsatellite DNA polymorphism. In criminalistics, dogs can be both participants in crime scenes in the form of attacks on humans or pets, and some witnesses through whose DNA extracted from their fur or feces, by DNA identification of a particular dog, it may be help to get out to the perpetrator or at least to the crime scene, which is also a good help in its disclosure. At the same time, population studies of dogs, during which the prevalence of certain alleles of marker traits in the form of STR loci in different territories is established, contribute to making the right decisions. The databases on STR-polymorphism of dog DNA or their prototypes are briefly described. Attention is paid to the sources of forensic canine DNA, as well as methods of its extraction and preliminary evaluation of isolated preparations. The use of VNTR polymorphism was rather short-lived, and was quickly replaced by STR polymorphism. There are some trends in the introduction of new polymorphic traits in this area in the form of single-nucleotide polymorphism or SNPs, potentially providing more accurate information, including for DNA identification of individuals. The issues of universal DNA certification of dogs are discussed, which can contribute to improving the culture of keeping dogs and will allow the elimination of stray dogs in the future, which will be humanistic character and potentially reduce the number of aggressor dogs.

Interaction among morphological, trophic and genetic groups in the rapidly radiating Salvelinus fishes from Lake Kronotskoe

Adaptive radiation in fishes entering novel post-glacial lakes ubiquitously gives rise to a set of typical forms specializing under the pressure of the same ecological gradients. The world’s most diverse flock of salmonids from Lake Kronotskoe (Kamchatka, N-E Asia) serves as a good model to study evolutionary divergence modes. Eight forms with different feeding types and habitat preferences are known to originate from Salvelinus malma. To determine the phasing of the flock radiation we analyzed morphometry, muscle isotope content, parasite fauna abundance and microsatellite DNA polymorphism in the sympatric forms inhabiting the lake. We found that seven out of eight morphologically independent forms can be distinguished by a stable feeding niche through comparing the stomach content, isotopic status and parasite fauna abundance. Five eco-morphs were found to be genetically independent, while three other morphs fell into one cluster without any significant restriction of the gene flow among the members. Partitioning of the resources in pelagic—benthic, epilimnetic—deepwater and lacustrine—riverine environments leads to divergence of the most genetically and morphologically distant forms. Smaller genetic and morphometric distances were found for the form pairs diverged along one or two of these gradients. The divergence of the last three eco-morphs in feeding tactics within the coastal zone is not associated with differentiation in microsatellite polymorphism suggesting a more recent and/or subtle specialization within this environment.

Exploring the Risks of Genetic Similarity Between Donor and Recipient in Human Leukocyte Antigen–Matched Transplantation

ObjectiveSuccessful allogeneic hematopoietic stem cell transplantation (HSCT) relies on human leukocyte antigen (HLA) matching. However, whether HLA-matching between donors and recipients increases recipients’ risk of genetic disease remains unclear. MethodsWe investigated whether HLA-matched donor cells used for HSCT have similar microsatellite DNA polymorphisms to HSCT recipients at 19 randomly selected loci including CSF1PO, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, PentaD, PentaE, TH01, TPOX, and VWA. We analyzed allele matching at each short tandem repeat (STR) loci in HLA-matched and mismatched (control) groups using binary outcomes and a quantitative numerical method. ResultsThe frequencies were similar between the HLA-matched group and the mismatched group for D6S1043. However, the allele matching rate was higher in the HLA-matched group than that in the mismatched group at 14 of the 19 STR loci. Overall, a significant increase in the rate of STR matching was observed in the HLA-matched group compared to the mismatched group (P = .004). ConclusionIt would be interesting to know if the HLA matched pairs came more often in question than their mismatched counterparts as candidates for fully HLA-matched unrelated HSCT. The actual risk for HSCT donors developing these diseases needs further evaluation.

Worker demography and behavior in a supercolonial ant colony: The case of the desert ant Cataglyphis niger

AbstractInsect societies headed by multiple queens (polygyny) raise evolutionary questions, such as how does genetic heterogeneity among colony members affect in‐nest interactions; or, are all queens equally reproductive or equally treated by workers? Answering such questions requires intensive and continuous observations of in‐nest behavior. Here, we addressed these questions in the polygyne supercolonial ant, Cataglyphis niger, using a barcoding system that enables the tracking of individual interactions, together with polymorphic DNA microsatellite markers that indicate the matriline and patriline of all individuals. Our findings that both queens and workers have low interrelatedness corroborate earlier reports regarding the supercolony structure of C. niger. Ovary inspection and worker genotyping revealed that all the queens contribute similarly to nest demography. Tracking positions of individual workers through time revealed that only a small proportion of them are constantly engaged in tending the queens and can be considered as retinue workers. However, genotyping these workers and the attended queens revealed no relationship to genetic relatedness, again typical of a true polygyne and supercolonial species. Unlike invasive supercolonial species, C. niger is native to Israel, enabling us to address questions regarding the driving forces, other than kin selection, that stabilize this society.

Microsatellite DNA Polymorphism of Channa marulius Inhabiting River Jhelum

Microsatellite DNA Polymorphism of Channa marulius Inhabiting River Jhelum

Pfcrt genotypes and related microsatellite DNA polymorphisms on Plasmodium falciparum differed among populations in the Greater Mekong Subregion

Malaria morbidity and mortality have decreased gradually in the Greater Mekong Subregion (GMS). Presently, WHO sets a goal to eliminate malaria by 2030 in the GMS. However, drug-resistant malaria has been reported from several endemic areas. To achieve the goal of elimination, the status of the emergence and spread of drug resistance should be monitored. In this study, the genotype of the Plasmodium falciparum chloroquine (CQ) resistance transporter gene (pfcrt) and 6 microsatellite DNA loci flanking the gene were examined. P. falciparum isolates (n = 136) was collected from malaria patients in Thailand (n = 50, 2002–2005), Vietnam (n = 39, 2004), Laos (n = 15, 2007) and Cambodia (n = 32, 2009). Amino acid sequences at codons 72–76 on the gene were determined. All of the isolates from Thailand were CQ-resistant (CVIET), as were all of the isolates from Cambodia (CVIET, CVIDT). Thirteen of the 15 isolates (87%) from Laos were CQ-resistant (CVIET, CVIDT), whereas the other 2 (13%) were CQ-susceptible (CVMNK). In contrast, 27 of the 39 isolates (69%) from Vietnam were CQ-susceptible (CVMNK), whereas the other 12 (31%) were CQ-resistant (CVIET, CVIDT, CVMDT) or mixed (CVMNK/CVIDT). The mean of expected heterozygosity of the microsatellite loci was 0.444 in the Thai population, 0.482 in the Cambodian population, and 0.734 in the Vietnamese population. Genetic diversity in the Thai population was significantly lower than that in the Vietnamese population. These results suggested that chloroquine selective pressure on P. falciparum populations is heterogeneous in the GMS. Therefore, further examination to understand the mechanisms behind the emergence and spread of drug-resistant malaria are needed.

Whole-exome sequencing reveals microsatellite DNA markers for response to dofetilide initiation in patients with persistent atrial fibrillation: A pilot study.

Dofetilide is a class III antiarrhythmic drug effective for the treatment of atrial fibrillation (AF). Dofetilide initiation (DI) associates with corrected QT interval (QTc) prolongation. Significant QTc prolongation during DI mandates dose adjustment or discontinuation of the drug. Microsatellite DNA are novel genetic markers associated with congenital and acquired health conditions. DNA microsatellite polymorphism may associate with QTc response to dofetilide initiation in patients with persistent AF. We performed whole-exome sequencing in a cohort of patients with persistent AF undergoing DI. Electrocardiographic variables and clinical data were assessed. We defined patients as eligible for DI when no significant QTc prolongation (>20% compared with baseline) was seen with a 500-μg dose. We defined patients as ineligible for DI when significant QTc prolongation was seen during DI with 500 μg. We investigated polymorphisms for 11 919 DNA microsatellite loci in relation to QTc response to DI. During the study, 14 consecutive patients with persistent AF presenting for DI were enrolled. Whole-exome sequencing revealed 14 different microsatellite loci in the 2 groups. All genes or proximal genes that harbor these loci are known to have expression in the human heart. Two genes, MYH6 and TRAK2, are known to have expression in the atria. TRAK2 is known to interact with KCNJ2, the inward-rectifier potassium channel 1. Microsatellite DNA polymorphisms seem to associate with QTc response to DI therapy in patients with persistent AF who are deemed otherwise eligible for dofetilide therapy.

Genetic structure of Apis mellifera carnica in Slovakia based on microsatellite DNA polymorphism

AbstractCarniolan honeybee (

Panmixia and Limited Interspecific Introgression in Coyotes (Canis latrans) from West Virginia and Virginia, USA.

The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci. These genotypes were compared with those from other canid populations to evaluate the extent of genetic introgression. We conducted spatial clustering analyses and spatial autocorrelation to assess genetic structure among sampled coyotes. Coyotes across the 2 states had high genetic diversity, and we found no evidence of genetic structure. Six to sixteen percent of individuals displayed some evidence of genetic introgression from other species depending on the method and criteria used, but the population possessed predominantly coyote ancestry. Our findings suggested introgression from other canid populations has played less of a role in shaping the genetic character of coyotes in these states compared with populations closer to the Canadian border. Coyotes appear to display a panmictic population structure despite high habitat heterogeneity and heavy human influence in the spatial environment, underscoring the adaptability of the species.

Analysis of microsatellite DNA polymorphism in the Tatra Shepherd Dog

ABSTRACTThe Tatra Shepherd Dog is one of five Polish native breeds of dogs originating from the Polish Tatra Mountains. The objective of the study was to determine genetic variation in a population of 60 dogs of this breed, based on polymorphism of 18 microsatellite (STR) markers, recommended by ISAG for canine parentage testing. The analysis showed considerable genetic variability in the studied loci. The 100 alleles identified in the test material were used to determine the polymorphism of the discussed markers. The highest polymorphism was found in the locus AHT171, in which 8 alleles were identified and PIC and HO values exceeded 0.8. The lowest polymorphism was detected for AHTk211, in which 3 alleles were determined, and PIC and HO values were 0.233 and 0.281, respectively. Average FIS had a low negative value, which suggests zero inbreeding of the studied breed. The probability of parentage exclusion estimated for the 18 markers totalled 99.996%.

Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

Microsatellite DNA polymorphism in selectively controlled Apis mellifera carnica and Apis mellifera caucasica populations from Poland

Genetic polymorphism in selectively controlled honeybee populations of A. m. carnica and A. m. caucasica in Poland, was characterized by microsatellite DNA analysis. All honeybee samples were analyzed for nine microsatellite loci: Ac011; A024; A043; A088; Ap226; Ap238; Ap243; Ap249 and Ap256, which were found to be polymorphic in both populations. The mean number of alleles per locus was 6.222 for A. m. carnica and 4.556 for A. m. caucasica. Average observed and expected heterozygosity values were calculated as 0.976 and 0.734 in A. m. carnica and as 0.933 and 0.603 in A. m. caucasica, respectively. For the nine microsatellite loci, a total of 76 alleles were found in both populations. Thirty-five private alleles were observed in A. m. carnica and 20 in A. m. caucasica. Information about allele frequencies, FST values and genotypic differentiation is given. Nei?s genetic distance between studied populations of A. m. carnica and A. m. caucasica was calculated as 0.384.

Genetic Differentiation among Populations of the Kurokashiwa Breed of Indigenous Japanese Chickens Assessed by Microsatellite DNA Polymorphisms

The Kurokashiwa breed of native Japanese chickens is primarily reared in Shimane and Yamaguchi Prefectures, Japan. To reveal the genetic diversity and differentiation among the Kurokashiwa populations in both prefectures, 29 microsatellites were analyzed. To prepare the microsatellites, 54, 55, and 24 blood samples were collected from the Kurokashiwa populations of five fancy breeders in Shimane Prefecture, three fancy breeders in Yamaguchi Prefecture, and the Livestock Technology Research Department, Yamaguchi Prefectural Agriculture and Forestry General Technology Center (LTRDY), respectively. The corrected number of alleles (allelic richness: AR) was considerably low (1.63-2.48) through all Shimane and Yamaguchi populations. However, inbreeding coefficient (F-IS) values were not significant in the entire Shimane and Yamaguchi ornamental populations as well as the LTRDY population. In addition, there was no statistically significant difference in expected heterozygosity (H-E) through all populations in Shimane and Yamaguchi Prefectures, although the H-E varied from 0.237 to 0.445 depending on populations. The topology of the phylogenetic tree, pairwise F-ST values, and STRUCTURE analysis indicated that Kurokashiwa populations were genetically separated between Shimane and Yamaguchi Prefectures. On the other hand, there was no genetic differentiation among ornamental populations within each prefecture, which seemed to have resulted from adequate random matings by exchanging individuals among fancy breeders within each conservation community, along with a proper random mating within LTRDY. The present study proposes a conservation strategy suggesting that the Kurokashiwa populations of Shimane and Yamaguchi Prefectures should be maintained separately with continuous exchange of birds within each conservation community to preserve genetic diversity. Also, the LTRDY population should be independently kept by avoiding matings with ornamental bird populations because it is a well established closed colony with a uniform genetic constitution.