Genetic structure of the water frog (Pelophylax esculentus complex) populations in the south of the Central Russian Upland

BACKGROUND: The water frog (Pelophylax esculentus complex) is hybrid in composition. In view of the fact that a large number of data on the species composition of the water frog and very scarce material on the genetic structure of populations are available in the literature, we aimed to analyze the genetic structure of populations of the water frog in the southern part of the Middle Russian upland, which was one of the refugia for many species during the glacial epoch and the center of dispersion in the postglacial time, based on DNA microsatellite markers. MATERIALS AND METHODS: The study involved 36 local populations. DNA variability was analyzed by multiplex SSR-PCR. Seven loci (Res 14, Res 15, Res 17, Res 22, Rrid059A, Rrid082A, and Rrid171A) were used for amplification. Fragment analysis of PCR products was performed on an ABI PRISM 3500 automated capillary DNA sequencer (Applied Biosystems, USA). RESULTS: The total number of alleles detected ranged from 13 to 41. The effective number of alleles (Ae) averaged 4.569 0.219, the Chenon index (I) 1.567 0.04, level of expected heterozygosity (Не) 0.68 0.01. According to Wrights model, the greatest contribution to genetic variability is made by the heterogeneity of individuals within populations, some of which are of a hybrid nature (Fis = 0.281 0.069, Fit = 0.413 0.053, Fst = 0.180 0.017). The average indicator of the intensity of gene exchange between populations (Nm) was 1.212 0.142 individuals per generation. The calculation of the effective abundance using the LD method indicates a high level of viability of the studied groups of the frogs. CONCLUSION: The results demonstrated a high level of genetic diversity and viability of most of the studied groups, which, due to the intense gene exchange between them, can represent a single panmictic population. The data of the genetic analysis support the active adaptation of P. esculentus complex to living in an urbanized environment.

Efficient PCR Amplification Protocol of Nuclear Microsatellites for Exuviae-Derived DNA of Cicada, Yezoterpnosia nigricosta

Although insect exuviae-based genetics is challenging, it can be a valuable method for obtaining reliable DNA resources by non-invasive sampling. This approach is especially effective when the target species is endangered/endemic or when sampling the adult is difficult. One example is cicadas, which during molt leave their exoskeletons on tree trunks, making them easily collectable. While cicada exuviae-derived DNA has previously been employed for mitochondrial DNA sequencing, this study aimed to develop a reliable method for the PCR amplification of nuclear microsatellite loci from cicada exuviae derived DNA for application in molecular ecology, conservation and population genetics. Five different PCR amplification protocols were performed, and the fragment patterns compared with those obtained using DNA extracted from adult individuals. Moreover, the relationship between the freshness of the exuviae and genotyping success was evaluated. TaKaRa LA Taq provided the best performance in the PCR amplification of DNA isolated from cicada exuviae and the electropherogram showed a clear fragment pattern that was equivalent to that obtained from the DNA extracted from the adult individual. This result suggests that cicada exuviae-derived DNA can be amplified by PCR and that multiple independent loci of nuclear DNA microsatellite markers can be easily genotyped. This study demonstrates that fresh cicada exuviae provide high quality DNA, which can be used for microsatellite genotyping. The methods developed in this study are applicable not only for cicada but other insect species for which exuviae are available. Thus, this study can make a significant contribution to insect sciences.

Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

PEMBENTUKAN POPULASI SINTETIS UNTUK PENINGKATAN KUALITAS GENETIK IKAN MAS

Benih ikan mas telah mengalami penurunan kualitas genetik yang menyebabkan penurunan performa fenotipik di lingkungan budidaya. Salah satu upaya perbaikan genetik adalah melalui pembentukan populasi sintetis yang merupakan penggabungan potensi genetik beberapa populasi plasma nutfah ikan mas. Penelitian ini bertujuan membentuk dan mengevaluasi performa genotipik dan fenotipik populasi sintetis ikan mas, yang merupakan penggabungan dari strain Rajadanu, Majalaya, Sutisna, Wildan, dan Sinyonya. Performa genotipik dievaluasi menggunakan metode mikrosatelit DNA, sedangkan performa fenotipik dievaluasi menggunakan analisis biometrik terkait kegiatan budidaya. Hasil penelitian menunjukkan bahwa nilai keragaman genetik populasi sintetis lebih tinggi 55,0%-287,5% dengan tingkat inbreeding 40,0%-77,14% lebih rendah dibanding populasi-populasi pembentuknya. Hal ini berdampak terhadap performa fenotipik populasi sintetis yang lebih baik, diindikasikan dengan peningkatan panjang, bobot akhir, dan tingkat produktivitas, masing-masing sebesar 2,5%-20,6%; 9,4%-61,8%; dan 18,2%-66,0% lebih baik dibanding populasi-populasi pembentuknya. Peningkatan kualitas genetik dan performa fenotipik populasi sintetis ini memberikan peluang untuk memperbaiki kualitas benih ikan mas pada kegiatan budidaya.Common carp in Indonesia has experienced a decline in genetic quality. The progressive decline leads to a significant decrease in carp performance in the farming environment. One of the efforts to genetically improve carp growth performance is through developing synthetic carp populations, which is a blend of the genetic potentials from several germplasm populations. This study aimed to form and evaluate the performance of genotypic and phenotypic of synthetic populations of common carp, blended from five strains of common carp, i.e., Rajadanu, Majalaya, Sutisna, Wildan, and Sinyonya. The genotypic performance was evaluated using the DNA microsatellite method. The phenotypic performance was assessed using biometric analysis, especially in terms of culture performance. The results showed that the genotypic performance of the synthetic populations of common carp was better than that of the founder strains. This performance was indicated by higher genetic diversity values, about 55.0%-287.5% and lower levels of inbreeding, about 40.0%-77.1%, compared with their founder populations. Phenotypic performance of the synthetic populations is also better than their founder populations, indicated by higher body length, weight, and productivity, about 2.5%-20.6%, 9.4%-61.8%, and 18.2%-66.0%, respectively. The improvement on genetic quality and phenotypic performance of the synthetic population provide opportunities to improve the quality of common carp fry in aquaculture activity.

Microsatellite instability (MSI, EMAST) in the pathogenesis of follicular lymphoma

Background. Genetic instability, an important phenomenon involved in oncogenic transformation and tumor progression, is associated with the insufficiency of the multicomponent DNA repair complex, in particular, the nucleotide mismatch repair (MMR) system. The MMR defect manifests itself as abnormalities in DNA microsatellite repeats, or microsatellite instability (MSI). In the studies of colorectal cancer, the role of MSI in prognostication of the disease, and defining the choice of specific therapy with immune checkpoint inhibitors has been proven.However, in lymphatic system tumors, the significance of this phenomenon is poorly understood. Determination of genetic instability in the onset of follicular lymphoma, a disease characterized by a heterogeneous course, may have prognostic value.Objective: to determine the genetic instability at the onset of follicular lymphoma.Materials and methods. Here we report an analysis of 24 microsatellite repeats and amelogenin loci in tumor cells of 46 follicular lymphoma patients.Results. In the studied cohort, lesions in microsatellite repeats were presented by MSI in 9 cases (19.6 %) and the loss of heterozygosity (LOH) in 19 cases (41.3 %). Most frequent lesions were found for the SE33 marker located at the q14 locus of chromosome 6. A significant association was shown between MSI and the double-hit follicular lymphoma group with rearrangements of the MYC and BCL2/BCL6 genes.Conclusion. Thus, our data indicate that the MSI phenomenon might be involved in the pathogenesis of the lymphatic tumors and particularly follicular lymphoma. However further studies on the expanded cohorts of patients are required to define the possible prognostic value of MSI in lymphatic tumors.

Intra- and interbreed genetic heterogeneity and divergence in four commercial pig breeds based on microsatellite markers

In recent years, there has been an increasing amount of attention paid to the genetic health of domesticated animals and its relationship with the level of inbreeding and genetic diversity. At the same time, insufficient attention is still paid to the study of intrabreed genetic diversity and intrabreed stratification. The main goal of our work was to analyze the intra- and interbreed genetic diversity of commercial pig breeds on the basis of DNA microsatellite (MS-DNA) polymorphism. In total, the work used data for 3,308 pigs, which represented 11 herds. The animals belonged to four commercial pig breeds – Duroc (DR), Yorkshire (YR), Landrace (LN) and Large White (LW). 12 microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (S0101, S0155, S0228, S0355, S0386, SW24, SW240, SW72, SW857, SW911, SW936, SW951) were used as DNA markers. When analyzing the intra- and interbreed variability of 11 herds, we found that all studied breeds significantly differed in terms of the proportion of both rare and the most common alleles. At the same time, the noted differences were determined, first of all, by the variability between individual herds within their breed. The location of herd centroids is random and is not consistent with their breed affiliation at all. When individuals belonging to the same breed are combined, the centroids of pig breeds in the space of first two axes from a Principal Coordinate Analysis form two clusters. The first one contains the only red pig breed (DR) used in the analysis, while the second one contains white pig breeds. In six pig herds the Ne estimates were below 50 inds., in two herds they were in the range of 50–100 inds., and finally in three herds the Ne estimates exceeded 100 inds. The analysis of the genetic variability of pigs of four commercial breeds showed that the high level of interbreed differences is caused, first of all, by the high variability among pig herds within each studied breed. Such intrabreed stratification can be formed due to the manifestation of many causes: different genetic basis of the founders of intrabreed genealogical groups, geographical isolation, different directions of selection within individual herds, exchange of animals between separate herds, the use of inbreeding in the practice of selection together with isolation, etc. Important consequences of intrabreed stratification are an increase in the level of interherd diversity (which is not lower than the level of interbreed diversity) against the background of a decrease in variability within individual herds, as well as a significant deficit of heterozygotes and an increase in the role of negative genetic and demographic processes. Thus, the existence of genetic heterogeneity within commercial pig breeds should be considered as an essential element in the history of their formation and breeding.

The way of value of Correlation of genomic DNA microsatellite loci and live weight of Chukchi reindeer

The article presents the genetic characteristic of the Chukchi reindeer breed. The object of the study was of the Chukchi reindeer. In recent years, the number of reindeer of the Chukchi breed has declined sharply. Reduced reindeer numbers could lead to biodiversity loss. The Chukchi breed of deer has good meat qualities, has high germination viability and is adapted in adverse tundra conditions of Yakutia. Herding of the Chukchi breed of deer in Yakutia are engaged only in the Nizhnekolymsky district. There are four generic communities and the largest of which is the agricultural production cooperative of nomadic tribal community «Turvaurgin», which was chosen to assess the genetic processes of breed using microsatellite markers: Rt6, BMS1788, Rt 30, Rt1, Rt9, FCB193, Rt7, BMS745, C 143, Rt24, OheQ, C217, C32, NVHRT16, T40, C276. It was found that microsatellite markers have a wide range of alleles and generally have a high informative value for identifying of genetic differences between animals and groups of animal. The number of identified alleles is one of the indicators of the genetic diversity of the population. The total number of detected alleles was 127. The Chukchi breed of deer is characterized by a high level of heterozygosity, and the random crossing system prevails over inbreeding in the population. On average, there were 7.9 alleles (Na) per locus, and the mean number of effective alleles (Ne) was 4.1. The index of fixation averaged 0.001. The polymorphism index (PIC) ranged from 0.217 to 0.946, with an average of 0.695.

Sociogenetic Organization of the Red Honey Ant (Melophorus bagoti)

Kin selection and inclusive fitness are thought to be key factors explaining the reproductive altruism displayed by workers in eusocial insect species. However, when a colony’s queen has mated with <2 males, workers may increase their fitness by producing their own male offspring. Conversely, when the queen has mated with ≥2 males, workers are expected to increase their inclusive fitness by eschewing the production of their sons and preventing other workers from reproducing as well. Here, we investigated sociogenetic structure and worker reproduction in the red honey ant, Melophorus bagoti. Morphometric analyses revealed that workers belong to one of two distinct subcastes: they are either majors or minors. Using DNA microsatellite markers, we showed that all the colonies had a single, multiple-mated queen and that there was no relationship between worker patriline and worker subcaste. Furthermore, we found that workers were producing males in the presence of the queen, which contrasts with the predictions of inclusive fitness theory. Although our results are based on a small sample, they can serve as the foundation for future research examining worker reproduction in M. bagoti.