Analysis of Geographic and Pairwise Genetic Distances Among Sheep Populations

This study assessed the usefulness of geographic and pairwise genetic distances in the characterization of five sheep populations using 15 microsatellite markers. The average F statistics across loci were F _IT = 0.523 ± 0.140, F _ST = 0.363 ± 0.131, and F _IS = 0.263 ± 0.092. The average heterozygosity was 0.716 ± 0.069, polymorphism information content was 0.691 ± 0.070, and effective number of alleles was 3.736 ± 0.998. Sheep populations clustered into group 1 (Hu and Tong breeds) and group 2 (small-tailed Han, Wadi, and Tan breeds). Reynolds’ distance varied from 0.0062 to 0.0499, and the range of gene flow (N _m) was 4.8834–40.0726 among the sheep populations. The results showed that the genetic structure of the five populations was not consistent with their genetic distances, and the population genetic divergence was not linearly related to geographic distance as indicated by a Mantel test (P = 0.7936).     

Microsatellite variability and differentiation of hatchery stocks of chum salmon Oncorhynchus keta Walbaum in Sakhalin

Variability at eight microsatellite loci was examined in five populations of chum salmon Oncorhynchus keta Walbaum from Sakhalin hatcheries. The population of Kalinino hatchery had the lowest heterozygosity and the lowest average number of alleles per locus. The populations examined exhibited significant differentiation, θ_ST = 0.026 on average per locus. The maximum genetic differences were found between the populations of the Kalinino and the Ado-Tymovo hatcheries; the latter differs from the remaining populations also by the highest number and high frequencies of specific alleles. The genetic features of the Taranai hatchery population, observed at microsatellite loci, reflect its “mixed” origin.     

Differentiation of four indian aboriginal cattle populations revealed by SIR markers

Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic Variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 ± 0.04 in Binjharpuri to 0.664 ± 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (F _IT) of 0.132 ± 0.03, was partly due to the genetic differentiation among breeds (F _ST = 0.044 ± 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F _IS = 0.094 ± 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei??s Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.     

Population genetic structure of the noxious weed Amaranthus retroflexus in Central Europe

Genetic variation was assessed in a range of populations of Amaranthus retroflexus using isoenzyme analysis. Population genetic diversity was measured by evaluating patterns of variation at six putatively neutral isoenzyme loci (comprising 24 putative alleles) within and among 20 populations of A. retroflexus collected in different habitats: ruderal habitats, cereal fields and hop gardens. Amaranthus retroflexus is a noxious weed of North American origin that infests various crops. Overall, A. retroflexus displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of polymorphic loci was 50.0%, with mean values of 2.01, 0.142 and 0.227 for the average number of alleles per polymorphic locus (A), observed heterozygosity (H_o) and expected heterozygosity (H_e), respectively. A discrepancy between observed and expected heterozygosity and significant differences from H-W expectation indicate that there is an excess of homozygotes in many populations. As a result, there is strong evidence of inbreeding within populations (F_IS = 0.382) and significant population differentiation (F_ST = 0.270). Even though the species is partly autogamous, inbreeding does not lead to strong inbreeding depression resulting from self-pollination, as inbreeding has no effect on the success of the species in today's countryside. Moreover, allele frequencies detected in agricultural habitats (i.e., cereal fields and hop gardens) differed from those detected in populations collected from ruderal habitats, which is probably caused by systematic application of herbicides in agricultural ecosystems.     

Population genetics of the common long-armed octopus Octopus minor (Sasaki, 1920) (Cephalopoda: Octopoda) in Chinese waters based on microsatellite analysis

Octopus minor (Sasaki, 1920) is a commercially important cephalopod in Chinese waters. To provide a theoretical basis for resource protection and sustainable management, we investigated genetic structure of ten O. minor populations in Chinese waters using microsatellite DNA markers. Eight microsatellite loci revealed high allelic diversity with 11–26 alleles per locus. Observed and expected heterozygosity varied from 0.412 to 0.900 and from 0.337 to 0.845, respectively. The overall F_ST value was 0.198, indicating great genetic differentiation among populations. The F_ST value between Yilan and other populations reached more than 0.3 that may be indicative of subspecies rank. Mantel test showed significant correlations between genetic and geographic distance (R = 0.383, P = 0.004) indicating that genetic differentiation of O. minor conformed to a pattern of isolation-by-distance. Using the Neighbor-joining method, cluster analysis divided nine populations into three groups and divided ten populations into two groups wherein Yilan was distinguished from the other populations. Analysis based on F_ST, D_c values and clustering highlighted the heterogeneity of Yilan and the relative homogeneity between Yilan and Ganyu. The significant population genetic structure of O. minor is related to the combined effects of geographical barriers, current features and life history characteristics.     

Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

Camel invokes fascinating chapter of Indian desert history and is integral component of its ecosystem. Camel population has reached a crisis point after three decades of decline (75%) causing major concern to the policy makers. >28% of Indian camel is not yet characterized. It is imperative to describe country’s camel germplasm and its existing diversity for designing conservation plan. One such population is Sindhi, distributed along border with Pakistan. Twenty five microsatellite markers being valuable tool for estimating genetic diversity were selected to elucidate genetic variability and relationship of Sindhi with two registered camel breeds of India- Marwari and Kharai. The standard metrics of genomic diversity detected moderate variability in all the three populations. A total of 303 alleles with a mean of 8.116 ± 0.587 alleles per locus were found in total of 143 animals. Sindhi population had intermediate allelic diversity with 8.522 ± 1.063 alleles per locus. Corresponding values in Marwari and Kharai were 8.783 ± 0.962 and 7.043 ± 1.030, respectively. Genetic variability within the breeds was moderate as evidenced by the mean observed heterozygosity of 0.556 ± 0.025. Sindhi camel population harbors higher genetic variability (Ho = 0.594) as compared to the two registered camel breeds (Marwari, 0.543 and Kharai, 0.531). Mean expected heterozygosity under Hardy-Weinberg equilibrium was higher than the observed values across the three camel groups, indicating deviations from assumptions of this model. In fact, average positive F value of 0.084 to 0.206 reflected heterozygote deficiency in these populations. These Indian camel populations have not experienced serious demographic bottlenecks in the recent past. Differences among populations were medium and accounted for 7.3% of total genetic variability. Distinctness of three camel populations was supported by all the approaches utilized to study genetic relationships such as genetic distances, phylogenetic relationship, correspondence analysis, clustering method based on Bayesian approach and individual assignment. Sindhi camel population was clearly separated from two registered breeds of Indian camel. Results conclude Sindhi to be a separate genepool. Moderate genetic diversity provides an optimistic viewpoint for the survival of severely declining indigenous camel populations with appropriate planning strategies for conserving the existing genetic variation and to avoid any escalation of inbreeding.     

Genetic differences between wild and hatchery populations of Korean spotted sea bass (Lateolabrax maculatus) inferred from microsatellite markers

The spotted sea bass, Lateolabrax maculatus, is popular in recreational fishing and aquaculture in Korea. Its natural population has declined during the past two decades; thus, beginning in the early 2000s stock-enhancement programs were introduced throughout western and southern coastal areas. In this study, genetic similarities and differences between wild and hatchery populations were assessed using multiplex assays with 12 highly polymorphic microsatellite loci; 96 alleles were identified. Although many unique alleles were lost in the hatchery samples, no significant reductions were found in heterozygosity or allelic diversity in the hatchery compared to the wild population. High genetic diversity (He = 0.724–0.761 and Ho = 0.723–0.743), low inbreeding coefficient (F _IS = 0.003–0.024) and Hardy–Weinberg equilibrium were observed in both wild and hatchery populations. However, the genetic heterogeneity between the populations was significant. Therefore, genetic drift likely promoted inter-population differentiation, and rapid loss of genetic diversity remains possible. Regarding conservation, genetic variation should be monitored and inbreeding controlled in a commercial breeding program.     

Genetic variation and relationships of eighteen Chinese indigenous pig breeds

Chinese indigenous pig breeds are recognized as an invaluable component of the world''s pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types, and three commercial breeds with 184 individuals. The observed heterozygosity, unbiased expected heterozygosity and the observed and effective number of alleles were used to estimate the genetic variation of each indigenous breed. The unbiased expected heterozygosity ranged between 0.700 (Mashen) and 0.876 (Guanling), which implies that there is an abundant genetic variation stored in Chinese indigenous pig breeds. Breed differentiation was shown by fixation indices (F_IT, F_IS, and F_ST). The F_ST per locus varied from 0.019 (S0090) to 0.170 (SW951), and the average F_ST of all loci was 0.077, which means that most of the genetic variation was kept within breeds and only a little of the genetic variation exists between populations. The Neighbor-Joining tree was constructed based on the Nei D_A (1978) distances and one large cluster with all local breeds but the Mashen breed, was obtained. Four smaller sub-clusters were also found, which included two to four breeds each. These results, however, did not completely agree with the traditional type of classification. A Neighbor-Joining dendrogram of individuals was established from the distance of – ln(proportions of shared alleles); 92.14% of the individuals were clustered with their own breeds, which implies that this method is useful for breed demarcation. This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.     

Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis

Twelve Chinese indigenous goat populations were genotyped for twenty-six microsatellite markers recommended by the EU Sheep and Goat Biodiversity Project. A total of 452 goats were tested. Seventeen of the 26 microsatellite markers used in this analysis had four or more alleles. The mean expected heterozygosity and the mean observed heterozygosity for the population varied from 0.611 to 0.784 and 0.602 to 0.783 respectively. The mean F_ST (0.105) demonstrated that about 89.5% of the total genetic variation was due to the genetic differentiation within each population. A phylogenetic tree based on the Nei (1978) standard genetic distance displayed a remarkable degree of consistency with their different geographical origins and their presumed migration throughout China. The correspondence analysis did not only distinguish population groups, but also confirmed the above results, classifying the important populations contributing to diversity. Additionally, some specific alleles were shown to be important in the construction of the population structure. The study analyzed the recent origins of these populations and contributed to the knowledge and genetic characterization of Chinese indigenous goat populations. In addition, the seventeen microsatellites recommended by the EU Sheep and Goat Biodiversity Project proved to be useful for the biodiversity studies in goat breeds.     

菲律宾蛤仔EST-SSRs标记开发及不同地理群体遗传多样性

利用13对微卫星引物对大连、莆田、青岛3个地理群体蛤仔遗传多样性进行了检测。结果表明:13个基因座共检测到154个等位基因,每个座位检测到的等位基因数在2-7个之间,平均有效等位基因数为2.7657;3个群体平均观测杂合度分别为0.4387、0.4194、0.2383,平均期望杂合度分别为0.6488、0.6484、0.5526;群体间的遗传多样性差异不显著(P＞0.05)。NJ聚类结果显示大连和莆田群体的蛤仔亲缘关系较近,二者与青岛群体关系较远。3个群体均有不同程度的偏离Hardy-Weinberg平衡现象,表明各群体基因频率和基因型频率的稳定性相对较低。本研究所获得的微卫星标记的多态信息含量(PIC)>0.5,说明这些微卫星位点的多样性较高,可为下一步遗传图谱构建研究提供参考。     

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H_E and H_O) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F_IS = 0.054, P < 0.001) and total inbreeding (F_IT = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F_ST) was 13.4%. The results of Bayesian model‐based clustering and a neighbour‐joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history.     

Variability of nuclear microsatellite loci in the populations of Siberian dwarf pine (<Emphasis Type="Italic">Pinus pumila</Emphasis> (Pallas) Regel) from the Russian part of the range

Variability of nuclear microsatellite loci was examined in Siberian dwarf pine. Six microsatellite loci (RPS2, RPS6, RPS12, RPS124, RPS127, Pc18) demonstrated different polymorphism levels in ten populations of Siberian dwarf pine. The average number of alleles per locus was 4.88, the average observed heterozygosity was 0.465, and the average expected heterozygosity was 0.510. About 13% of total genetic variability was explained by the genetic differences between the populations (F _ST = 0.129). Genetic distances between the examined populations of Pinus pumila inferred from the data on the SSR marker frequencies statistically significantly correlated with the geographical distances between the population samples. The level of genetic variability of the populations from Kamchatka Peninsula was lower than that demonstrated by continental and island populations. The genetic differentiation of the Kamchatka–Magadan and other populations of Siberian dwarf pine observed in our study can be explained in terms of their formation from different Pleistocene refugial centers.     

Genetic diversity and molecular differentiation of Chinese toad based on microsatellite markers

Genetic diversity and population structure of 9 populations of Bufo gargarizans with total 111 samples in China were assessed using seven microsatellite loci. The analysed microsatellite markers produced 161 alleles, varied from 9 to 38 alleles each locus. The number of alleles per population per locus ranged from 4.43 to 10.29. Polymorphic information content showed that all seven loci were highly informative (mean = 0.810 ± 0.071). The average observed heterozygosity was less than the expected (0.353 ± 0.051 and 0.828 ± 0.067, respectively). All tested populations gave significant departures from Hardy–Weinberg equilibrium. Genetic differentiation among the populations was considerably high with the overall and pairwise F _ST values (mean = 0.160 ± 0.039), and showed fairly high level of inbreeding (indicated by a mean F _IS value of 0.504 ± 0.051) and global heterozygote deficit. In comparison to other amphibian studies; however, our results suggested that the level of genetic structuring in B. gargarizans was relatively low in the geographical scale of the study area. Interestingly, the speculated population bottleneck was found to be absent and the analyses provide only weak evidence for a recent contraction in size even though there was severe inbreeding (indicated by the F _IS value) in the Chinese toad populations.     

Isolation and characterization of microsatellite markers in the tetraploid birch,Betula pubescens ssp. tortuosa

The mountain birch, Betula pubescens ssp. tortuosa is a tetraploid tree species which forms the tree limit in northern Fennoscandia. We identified nine polymorphic microsatellite loci in order to characterize the genetic structure of populations at different elevations close to the treeline. The microsatellite loci were highly polymorphic, with 14–42 alleles per locus and an average expected heterozygosity of 0.73 ± 0.25 under random chromosome segregation and 0.68 ± 0.23 under random chromatid segregation.     

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

Isolation and characterization of 15 polymorphic microsatellite markers for the fig-pollinating wasp,Blastophaga nipponica (Hymenoptera: Agaonidae)

We developed microsatellite markers for the fig-pollinating wasp Blastophaga nipponica Grandi using a dual-suppression-PCR technique. Twenty-one candidates of microsatellite loci were obtained, of which 15 yielded scorable patterns. The degree of polymorphism for the 15 loci was further characterized using summary statistics describing the genetic variation in 60 individuals from three natural populations in Japan. All 15 loci were polymorphic and yielded 2–27 alleles per locus. Overall observed heterozygosity (H _O) and expected heterozygosity (H _E) were 0.465 and 0.631, respectively. As expected, based on the inbreeding tendency of this species, the mean inbreeding coefficient (F _IS) was high (= 0.255). These markers will contribute to studies on the population structure of this species.     

Genetic diversity analysis by microsatellite markers in four captive populations of the sika deer (Cervus nippon)

The Chinese sika deer (Cervus nippon) is a rare and vulnerable animal in China for medical use. In this study, the genetic diversity and population genetic structure of 113 Chinese sika deer from 4 populations (Linyi Farm, LF; Linyi Park, LP, Yangzhou Farm, YF; Yangzhou Zoo, YZ) were investigated with 14 microsatellite loci. Eighty-three alleles were detected at the 14 loci in all populations. The expected heterozygosity ranged from 0.257 to 0.863 and the observed heterozygosity from 0.226 to 0.821. The polymorphism information content at different loci ranged from 0.217 to 0.825. The results of the HWE (Hardy–Weinberg equilibrium) tests indicated that only four loci (CEH-5, BL42, Mber70, and CEH-2) were in HWE (P > 0.01). The mean number of alleles per population ranged from 3.21 to 5.64, observed and expected heterozygosities ranged from 0.568 to 0.685, respectively. Positive inbreeding coefficient (F_IS) values were found in every population. F_ST values ranged from 0.101 in the LF to 0.155 in the YZ. The genetic identity ranged from 0.1236 to 0.1645. The genetic distance ranged from 0.4746 to 0.6025. The results of this study indicate moderate genetic variation and polymorphism across the loci. Appropriate breeding strategies should be designed for deer in captivity.     

Genetic Polymorphism of Microsatellite DNA in Two Populations of Northern Sheatfish (Silurus soldatovi)

In this article, population variations and genetic structures of two populations of northern sheatfish (Silurus soldatovi) were analyzed using 24 microsatellite loci enriched from southern catfish (S. meriaionalis Chen) by magnetic beads. Gene frequency (P), observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information contents (PIC), and number of effective alleles (Ne) were determined. One population was wild, ripe individuals collected from Heilongjiang River (HNS); the other was cultured fry collected from Songhuajiang River (SNS). The Hardy-Weinberg equilibrium (HWE) was tested by the genetic departure index (d). The coefficient of gene differentiation G_ST and Φ_ST by AMOVA (Analysis of Molecular Variety) was imputed using Arlequin software in this study. In addition, a phylogenetic tree was constructed by UPGMA method based on the pairwise Nei's standard distances using PHYLIP. A total of 1 357 fragments with sizes ranging between 102 bp and 385 bp were acquired by PCR amplifications. The average number of alleles of the two populations was 8.875. Results indicated that these microsatellite loci were highly polymorphic and could be used as genetic markers. The mean values of the parameters P, Ho, He, PIC, and Ne were 0.165, 0.435, 0.758, 0.742, and 5.019 for HNS and 0.147, 0.299, 0.847, 0.764, and 5.944 for SNS, respectively. Although there were differences, there were no significant differentiations except for the locus HLJcf37. These populations to a certain extent deviated from HWE, such as excessive and deficient heterozygote numbers. The value of G_ST was 0.078 and above 98% of the variation were differences among individuals within the population, so the variation between populations was insignificant. Cluster analysis also showed that the relationships among individuals were very close. In conclusion, the microsatellite markers that were developed through this study are useful for genetic analysis and the genetic culture that was proposed in this study has no significant impact on S. soldatovi.     

Genetic structure of Arabian Peninsula dromedary camels revealed three geographic groups

Dromedary camels (Camelus dromedarius) are widespread in the desert and semi-desert areas of Africa, the Arabian Peninsula, some parts of southwest Asia and Australia. In the Arabian Peninsula, these well-adapted species have been classified based on their ecology into Desert camels, found mainly in the north and center of the Peninsula, Mountain camels, distributed along the west and south of the Peninsula, and Beach camels, populating the west to southwest of the Peninsula. Here, we aimed to investigate the genetic relationship between 386 camels corresponding to 12 dromedary populations from different geographical locations and ecology in the Arabian Peninsula with the genotyping of 17 microsatellite loci. No significant deviation was observed in heterozygosity, allelic richness, Fis (inbreeding coefficient) among the studied populations had a mean value of 0.5849, 4.808 and 0.04, respectively. A mean Fst (fixation index) value of 0.0304 was calculated for the various populations with the highest value obtained between racing Omani and Awarik camel populations (0.079). Both the neighbor-joining phylogenetic tree and the STRUCTURE analysis divided the populations into three different groups corresponding to their Arabian Peninsula geographic location (North, Central and West, South-West, and South-East of the Arabian Peninsula), rather than their ecological classification, with a high level of genetic admixture and gene flow among them. Investigating the genetic relationship of dromedary populations in the Arabian Peninsula can be considered as the first milestone to conserve this well-adapted species. The results obtained here need to be further validated using whole genome sequencing data.     

Heterozygote excess through life history stages in Cestrum miradorense Francey (Solanaceae), an endemic shrub in a fragmented cloud forest habitat

Comparisons of genetic diversity and population genetic structure among different life history stages provide important information on the effect of the different forces and micro‐evolutionary processes that mould diversity and genetic structure after fragmentation. Here we assessed genetic diversity and population genetic structure using 32 allozymic loci in adults, seeds, seedlings and juveniles of eight populations of the micro‐endemic shrub Cestrum miradorense in a highly fragmented cloud forest in central–eastern Mexico. We expected that due to its long history or rarity, this species may have endured the negative effects of fragmentation and would show moderate to high levels of genetic diversity. High genetic diversity (H_e = 0.445 ± 0.03), heterozygote excess (F_IT = ?0.478 ± 0.034, F_IS = ?0.578 ± 0.023) and low population differentiation (F_ST = 0.064 ± 0.011) were found. Seeds had higher genetic diversity (H_e = 0.467 ± 0.05) than the later stages (overall mean for adults, seedlings and juveniles H_e = 0.438 ± 0.08). High gene flow was observed despite the fact that the fragmentation process began more than 100 years ago. We conclude that the high genetic diversity was the result of natural selection, which favours heterozygote excess in all stages, coupled with a combination of a reproductive system and seed/pollen dispersal mechanisms that favour gene flow.