Evaluation of the genetic structure of the Polesskaya horse population

For the Republic of Belarus, development of a forensic reference database on the basis of 18 autosomal microsatellites (STR) using a population dataset (N = 1040), “familial” genotypic dataset (N = 2550) obtained from expertise performance of paternity testing, and a dataset of genotypes from a criminal registration database (N = 8756) is described. Population samples studied consist of 80% ethnic Belarusians and 20% individuals of other nationality or of mixed origin (by questionnaire data). Genotypes of 12346 inhabitants of the Republic of Belarus from 118 regional samples studied by 18 autosomal microsatellites are included in the sample: 16 tetranucleotide STR (D2S1338, TPOX, D3S1358, CSF1PO, D5S818, D8S1179, D7S820, THO1, vWA, D13S317, D16S539, D18S51, D19S433, D21S11, F13B, and FGA) and two pentanucleotide STR (Penta D and Penta E). The samples studied are in Hardy–Weinberg equilibrium according to distribution of genotypes by 18 STR. Significant differences were not detected between discrete populations or between samples from various historical ethnographic regions of the Republic of Belarus (Western and Eastern Polesie, Podneprovye, Ponemanye, Poozerye, and Center), which indicates the absence of prominent genetic differentiation. Statistically significant differences between the studied genotypic datasets also were not detected, which made it possible to combine the datasets and consider the total sample as a unified forensic reference database for 18 “criminalistic” STR loci. Differences between reference database of the Republic of Belarus and Russians and Ukrainians by the distribution of the range of autosomal STR also were not detected, corresponding to a close genetic relationship of the three Eastern Slavic nations mediated by common origin and intense mutual migrations. Significant differences by separate STR loci between the reference database of Republic of Belarus and populations of Southern and Western Slavs were observed. The necessity of using original reference database for support of forensic expertise practice in the Republic of Belarus was demonstrated.

Purpose: study of associations of live weight and genotypic traits in reindeer populations.Materials and methods. The studies were carried out in 2018-2020. on the basis of 8 agricultural enterprises in Chukotka. Tissue samples (ear pinch) of deer of different sex and age groups served as material for genetic studies. In molecular genetic studies, 1002 samples were used. Individual genotyping of animals was carried out using the ISSR-PCR method. The live weight of the reindeer was determined using the materials of the zootechnical reports of the reindeer farms. Associations of the average population indices of genetic diversity and live weight of deer were established by a calculation-statistical method of comparing the values of values. The correlation coefficient was calculated by the product method according to the Pearson formula.Results. The variability of ISSR markers in populations indicates a significant similarity between them in most of the allelic frequencies, which confirms the common origin, economic and breeding use of the Chukchi breed deer. The populations are characterized by a high degree of heterogeneity. Differences in live weight between highly productive and less productive populations on average for all sex and age groups of deer amounted to 16.8%. At the same time, the populations with a high live weight of deer significantly exceeded the populations with a lower live weight in the average number of alleles per locus by 5.0% (P <0.01), the number of effective effective alleles - by 11.8% (P <0.001), polymorphic information content index (PIC) - by 35.8% (P <0.01). The homozygosity coefficient in the low-productive animals was 12.6% higher than in the high-productive group. In the populations with the highest live weight of deer - WZR, WAE and AMG, the most significant indicators of genetic diversity were also found: the average number of alleles per locus is 8.57; 10.45 and 8.71; effective alleles per locus - 7.57; 9.10 & 8.15; expected heterozygosity - 0.868; 0.890 & 0.877; PIC index - 0.248; 0.380 and 0.374, respectively. In populations with a low live weight of deer - OST and CHN, the smallest values of the number of active effective alleles per locus were found - 6.68 and 6.41; expected heterozygosity - 0.850 and 0.844, PIC index (proportion of heterozygotes) - 0.151 and 0.254. The correlation coefficient between the indicator of live weight and the genetic diversity of deer turned out to be equal for the average number of alleles per locus r = 0.335; the number of effective alleles - r = 0.52; heterozygosity - r = 0.558, the proportion of heterozygous variants - r = 0.646.Conclusion. The data obtained make it possible to state the existence of a dependence of the live weight of deer on the genotypic diversity in the populations of the Chukchi breed.

The aim of this study was to analyze the genetic variability and population structure of the Landrace population by using 12 microsatellite markers. A total of 90 pigs representing one commercial breed (Landrace) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936 SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by FAO/ISAG. GenAIEx software was used to calculate the allele frequencies, effective number of alleles (Ae), observed (Ho) and expected (He) heterozygosity, within-population inbreeding estimate (Fis), Shannon’s information index (ISh). Overall allele frequency values ranged from 0.006 to 0.9333 (at allele SW951120). The number of observed alleles (Na) detected ranged from 5 (S0155 and SW911) to 13 (SW72), with an overall mean of 9.00 ± 0.80 and a total of 108 alleles were observed at these loci. However, the effective number of alleles (Ae) ranged from 1.57 (SW951) to 5.49 (SW240) with a mean of 3.29 ± 0.33. Shannon’s information index (ISh) which measures the level of diversity, was sufficiently high – from 0.79 (for SW951) to 2.01 (for SW240) – with a mean of 1.43 ± 0.09. The overall means for observed (Ho) and expected (He) heterozygosities were 0.578 ± 0.009 and 0.662 ± 0.004, respectively, which ranged from 0.307 (SW951) to 0.814 (SW857) and 0.361 (SW951) to 0.818 (SW240), respectively. Of the 12 microsatellites analyzed using Fisher’s exact test, 50% were in Hardy-Weinberg equilibrium, and 6 were out of equilibrium (P < 0.05). Three mutation models namely, infinite allele model (I.A.M.), two phase model (T.P.M.), stepwise mutation model (S.M.M.) were estimated using the BOTTLENECK software. The results are indicated that the Landrace pig population is non-bottlenecked and remained at mutation-drift equilibrium. The study stands first in genetic characterization of the Ukrainian Landrace pig population through microsatellite markers. The various parameters and values used to quantify genetic variability, such as the high mean (and effective) number of alleles and the expected and observed heterozygosities, indicated high genetic variability in the Ukrainian Landrace pigs. The population has not undergone any recent and/or sudden reduction in the effective population size and remained at mutation-drift equilibrium.

In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations.

In this study, we presented a panel of 14 microsatellite loci (MFW1, MFW2, MFW6, MFW9, MFW10, MFW11, MFW13, MFW16, MFW20, MFW24, MFW26, MFW28, MFW29 and Cid0909), with which we studied the genetic structure of Cyprinus carpio carpio of the breed “Izobelinsky” in the Republic of Belarus. Four offshoots of carp were included in the study: two mirrory (“Smes’ zerkal’naya”, “Tri prim”) and two scaly (“Smes’ cheshujchataya”, “Stolin XVIII”).As a result, it was found that the carp breed “Izobelinsky” exhibits a high level of in-breed genetic variability. In the studied microsatellite loci, 231 alleles were identified, 62 % of the total number of alleles were rare alleles with a frequency of occurrence of less than 5.0 %. The number of effective alleles (Ne) at the loci ranged from 3.082 (MFW10) to 9.754 (MFW26). The Shannon biodiversity index (I) was 2.082 ± 0.075. The highest value of the expected heterozygosity index (He) was noted for the MFW26 locus (0.897), the lowest – for the MFW10 locus (0.676).The greatest genetic diversity is characteristic of the scaly carp “Smes’ cheshujchataya” and “Stolin XVIII”. The highest total percentage of rare alleles was determined for fishes from “Stolin XVIII”. The minimum values of this parameter were found for specimens of the carp “Smes’ zerkal’naya” and “Tri prim”.The results of this study indicate a fairly high genetic diversity of four offshoots of the carp breed “Izobelinsky”, which was established using the marker loci optimally selected for analysis. This makes it possible to differentiate the layering among themselves.

BANK OF ANIMAL GENETIC RESOURCES OF INSTITUTE OF ANIMALS BREEDING AND GENETICS ND. A. M.V.ZUBETS OF NAAS SYSTEM OF ANIMAL BIODIVERSITY CONSERVATION OF UKRAINE

The study assessed the genetic diversity of commercial varieties and feral populations of oilseed rape (Brassica napus L.) grown in the Republic of Belarus according to the genotyping data of 7 microsatellite loci – Na12D08, Ol12D04-1, Ol12D04-2, Ra2A05, Na10H03, Na14H11, Ol11B05. The following parameters were calculated: the average number of alleles per locus, the effective number of alleles, the levels of expected and observed heterozygosity, % of polymorphic loci. The results indicate a greater genetic diversity in feral oilseed rape populations. According to the cluster analysis, one feral population fell into a cluster of commercial varieties and demonstrated similarities with the variety Atora, which indicates its recent wildness and the preservation of the genetic characteristics inherent in cultivated varieties. The variety Mercedes was clustered together with samples of feral populations, which may indicate its hybrid origin. An analysis of the structure of the genotype distribution in the Structure software showed the division into three clusters – commercial varieties, feral populations and samples of B. rapa. The established genetic divergence between feral populations and commercial varieties indicates that feral oilseed rape is able to maintain persistent populations inBelarus. In practice, this should be taken into account while assessing the environmental risk when transgenic rape is released into the environment. When cultivating transgenic rapeseed, special attention should be paid to measures to prevent the occurrence of its free-growing populations.

Genetic Structure of Native Sheep Populations in East and South Asia

The article highlights the main achievements, problems and directions of the further development of the landing stock of Ukraine, the prospects of scientific research of Institute of Animal breeding and Genetics nd. a. M.V.Zubets of the NAAS in the areas of breeding, genetics, biotechnology of reproduction and preservation of the gene pool of farm animals. Institute is the initiator of four dairy herds (Ukrainian Red-and-White, Black-and-White, Red and Brown dairy bread) and four meat (Ukrainian, Volyn, Polissya and Southern meat) breeds of cattle. Its employees carry out scientific support of regional livestock development programs, development of systems for the creation and management of commercial herds of dairy and beef cattle, which contributes to solving the global food problem, and to ensure the nutrition security of Ukrainian population. The newly created Ukrainian Black-and-White, Red-and-White and Red dairy breeds for the predominantly intra-species breeding improvement and limited access to the gene pool of the Holstein breeding breed should remain the main areas of the breeding improvement of domestic dairy cattle breeding. The existing breeding system in cattle in Ukraine does not meet international standards and practically does not work in a complex way, and it threatens the final destruction of domestic breeding livestock, a significant dependence of the country on the import of breeding resources. To solve the problem, a new structure of the breeding service with a clear definition of the organizational basis for the management of tribal affairs and functional responsibilities of the subjects of its implementation was proposed, the formation of a centralized national information base for the identification, registration, origin and performance of animals, the keeping of state books of breeding animals as the basis estimation of their genetic value, and its realization is entrusted to the state enterprise created at the institute on Main scientific-production informational-elective center in livestock. Promising areas for farm animal breeding research are grouped into gene identification and the degree of development of quantitative attributes (QTL), early prediction and evaluation of breeding value of animals using markers (MAS). Research on molecular genetics is aimed at improving genetic analysis methods at individual and population levels, monitoring herds of cattle according to different types of genetic markers. Genetic systems for testing animals in 9 loci quantitative attributes, which are involved in the formation of qualitative indicators of dairy and meat productivity. A work is under way to test animals for the polymorphism of the BoLA-DRB3 gene of the major histocompatibility complex in animal populations for resistance to or susceptibility to mastitis. Biotechnology research focuses on reproductive biology methods, first of all, manipulations with gametes of farm animals, in vitro fertilization of pre-matured oocytes of cows and pigs, and others. The technology of obtaining oocyte cumulus complexes from ovaries of animals, the conditions of their storage, cultivation and fertilization out of the organism, which allows receiving a much larger number of embryos for both scientific and practical purposes, is developed. A separate direction is the work to improve the biotechnological methods of reproduction of farm animals using nanomaterials. It is based on the application in cryopreservation and sperm production of sperm and ovules of various variants of biologically active substances that are applied to highly dispersed silica molecules (albumin of blood serum of cattle, N-acetylneuramic acid – UFS / BSA / NANA). In order to monitor and preserve the diversity of genetic resources of agricultural animals in Ukraine, a complex of works under NAAS scientific program "System of work in populations and preservation of biological diversity of genetic resources of farm animals" ("Preservation of gene pool of breeds") with a coordination center on the basis of Institute of Animal breeding and Genetics nd. a. M.V.Zubets of NAAS. The research resulted in the development of the Program for the preservation of the gene pool of local and endangered breeds of farm animals in Ukraine for 2017–2025, in which the methodological bases for preservation of the gene pool were generalized, animal breeds were classified according to the criteria of risk, the minimum sizes of herds (real and virtual) of faulting species were substantiated, the minimum the size of subsidies for the proper functioning of small-numbered breeds, general methodological approaches to assessing the specificity of genetic resources are specified.

Commercial panels of microsatellite (STR) loci are intended for DNA analysis of the domestic dog (Canis lupus familiaris) and, therefore, when genotyping the Grey wolf (Canis lupus lupus), most markers reveal significant deviations from the Hardy-Weinberg equilibrium and have a low informative value, which complicates their use in a forensic examination. The aim of this study was to select STR markers that equally effectively reflect population polymorphism in the wolf and the dog, and to create a universal panel for the identification of individuals in forensic science. Based on the study of polymorphisms of 34 STR loci, a CPlex panel of 15 autosomal loci and two sex loci was developed, which is equally suitable for identifying wolfs and dogs. Analysis of molecular variance (AMOVA) between samples revealed significant differentiation values (FST = 0.0828, p < 0.05), which allows the panel to be used for differentiating between wolf and dog samples. For the first time in the forensic examination of objects of animal origin in the Republic of Belarus, population subdivision coefficients (θ-values) were calculated for each of the 15 STR loci of the test system being reported. It was shown that the values of the genotype frequency, when averaged over all studied animals without and with considering the θ-value, differ by three orders of magnitude (3.39 · 10-17 and 4.71 · 10-14, respectively). The use of population subdivision coefficients will provide the researcher with the most relevant results of an expert identification study. The test system was validated in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods. A computational tool was developed to automate the analysis of genetic data on the wolf and dog in the forensic examination; two guides were approved for practicing forensic experts. This methodology is being successfully used in expert practice in investigating cases of illegal hunting, animal abuse and other offenses in the Republic of Belarus.

Twelve microsatellite loci were used to investigate genetic diversity and population structure of common carp,Cyprinus carpio from Yuan River(the upper reaches of Red River in Yunnan Province,China).One hundred and ninety two samples of adult common carp were collected in 2011 from five sampling points.A total of 201 alleles were detected over all loci and the number of alleles per locus ranged from 2 to 27.There were 113 low frequencies alleles at the frequencies less than 0.05.Mean number of alleles(NA) ranged from 12.25 to 14.67 per locus per population,effective number of alleles(NE) ranged from 8.28 to 9.73,mean observed heterozygosity(HO) and mean expected heterozygosity(HE) at the 12 loci ranged from 0.7765 to 0.8037,and from 0.7761 to 0.8080,and mean polymorphism information content(PIC) ranged from 0.7534 to 0.7843.Mean number of alleles(NA),mean effective number(NE) of alleles,mean observed heterozygosity(HO),mean expected heterozygosity(HE) and mean polymorphism information content(PIC) were 16.50,11.26,0.7927,0.8049,0.7966 respectively for overall samples.The result indicated that the genetic diversity of common carp from Yuan River was abundant.An analysis on the distribution of genetic variation(AMOVA) indicated that the variation within population was very high(95.87%),while among populations was low(1.69%).The value of fixation index and gene flow were 0.0256,9.5003 respectively for overall samples.Nei′s unbiased measures of genetic identity and genetic distance among populations rang from 0.8632 to 0.9700,0.0305 to 0.1471 respectively.This suggests that there were high genetic similarity among the 5 populations and significant genetic differentiations among the common carp individuals from Yuan River.So,the common carp from Yuan River should be managed by a population management unit.The genetic background of artificial stocking of carp larvae should not only be taken into consideration in fisheries enhancement,but also a system of evaluating the stock enhancement effectiveness should be established to prevent losing genetic biodiversity.

The knowledge about the level of genetic diversity and population structure in natural populations of Artemisia annua L. is a primary step in breeding programs for development of new cultivars with higher artemisinin level and better quality of secondary metabolites composition. We used PCR-based “retrotransposon-microsatellite amplified polymorphisms” (REMAPs) to study insertional polymorphism in A. annua genome to assess genetic variability and population structure in a collection of 118 accessions collected from north and northwest of Iran. Twenty-five primer combinations of 10 retrotransposon and seven ISSR primers amplified a total of 693 clear and unambiguous fragments in the studied accessions. The average number of bands, polymorphic bands, polymorphism, effective number of alleles, Shannon’s information index and expected heterozygosity were 27.72, 24.76, 88.14%, 1.47, 0.42 and 0.28, respectively. The analysis of molecular variance revealed high genetic variation present within sampled geographical regions. Distance-based cluster analysis assigned the studied accessions into four clusters according to their geographical origin, which were also confirmed by principal coordinate analysis. In model-based Bayesian clustering, the maximum value of Δk was obtained when the collection of 118 assayed A. annua accessions assigned into two subgroups (K = 2). The results showed the high genetic variation in the collection of Iranian sweet wormwood which revealed by REMAP markers indicating the reliability and efficiency of this marker system for analysis of genetic diversity and population structure of A. annua.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40415-022-00860-x.

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age‐0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density‐dependent factors. An isolation‐by‐distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic diversity and stocking appeared to alter allelic frequencies and the genetic structure of Walleye populations in Wisconsin, possibly resulting in disruption of local adaptation.

Simple SummaryThe aim of this study is to reveal the genetic variability and population structure of maternal lines of the Polish Konik—a native Polish horse breed of the primitive type included in the Polish conservation programme. The analysis was carried out on the basis of 17 microsatellite markers routinely used for parentage testing. The structural analysis indicated the likelihood of three genetic clusters (using the Structure and Structure Harvester software). F-statistics indicated a low level of inbreeding. All mean population coefficients were close to those obtained for representatives of male founder lines. The population seemed to be stable. However, due to a previous bottleneck event, breeding strategies should focus on avoiding inbreeding depression, preventing the decrease of genetic variability, and sustaining the active female lines.The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines as possible. The Polish Konik, a native Polish primitive-type horse breed and is one of the breeds included in such a programme in Poland. Presently, there are only 16 (of the 35 maternal lines known in 1962), some of which are endangered. We examined the genetic variability and structure of the Polish Konik maternal lines (176 individuals) on the basis of the pedigree data and 17 microsatellite markers (STRs) from parentage testing. The overall mean number of alleles was 7.647 (±0.411), the effective number of alleles was 3.935 (±0.271), the mean number of alleles for which the frequency was equal to or lower than 5% was 4.471 (±0.286), and the mean information index was 1.506 (±0.087). The structure of the population and admixture patterns were calculated with the Structure and Structure Harvester software. The structural analysis indicated three likely genetic clusters; as the most optimal K value was estimated as 3, with ∆K of 15.4188. The F-statistics results indicated a low level of inbreeding (average inbreeding coefficient FIT was 0.0188, coefficient of differentiation FST was 0.0304, and mean inbreeding index value FIS was −0.0119). Variability monitoring should be carried out in order to avoid inbreeding depression, while breeding strategies should be designed to prevent the decrease of genetic variability in the Polish horse breed and to sustain the active female lines.