Isolation and characterization of microsatellite loci in Tripterygion delaisi

We isolated 49 microsatellite loci from a genomic library of Tripterygion delaisi×anthosoma enriched for CA and GA repeats. Ten loci were screened in 30 individuals with high numbers of alleles per locus (averaging 15.5 ± 2.86) and observed heterozygosity (averaging 0.765 ± 0.052). No deviations from Hardy–Weinberg expectations were detected. These highly polymorphic markers will be useful in determining the spatial patterns of genetic diversity between and within subspecies of Tripterygion delaisi.     

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.     

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.     

Restoration of a bighorn sheep population impeded by Mycoplasma ovipneumoniae exposure

Bighorn sheep (Ovis canadensis) were once extirpated from the Black Hills region of South Dakota, U.S.A., mirroring declining populations throughout North America. Since the 1960s, several reintroductions have occurred in the Black Hills to reestablish populations, with varying success. We translocated 26 bighorn sheep from Alberta, Canada, to the Black Hills (February 2015) to restore bighorn sheep to their historic range. Due to prior examinations of cause‐specific survival, subsequent genetic diversity and disease prevalence analyses were required to evaluate success of the restoration effort. We measured a mean allelic diversity of 5.23 (SE = 0.44 [mean number of alleles]) and an observed heterozygosity of 0.71 (SE = 0.06; expected = 0.64 ± 0.05) in the translocated individuals. Translocated bighorn sheep tested negative for Mycoplasma ovipneumoniae at capture. An autogenous vaccine was administered prior to release in an attempt to safeguard the translocated bighorn sheep from infection with a strain known to be resident in adjacent bighorn sheep populations. However, the year following the translocation, a different strain of M. ovipneumoniae was associated with a pneumonia outbreak that resulted in 57.9% mortality. Our results suggest that allelic diversity and heterozygosity were sufficient for long‐term herd establishment, reducing the potential for founder effects. However, the overwhelming mortality associated with pneumonia, via the transfer of M. ovipneumoniae from an unknown source, limited the success or our reintroduction efforts. Successful attempts to restore bighorn sheep to their historic ranges must consider and mitigate potential routes for M. ovipneumoniae transmission pre‐ and post‐reintroduction.     

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.     

Development and characterization of microsatellite markers in the Colorado potato beetle,Leptinotarsa decemlineata

The characterization of 11 Leptinotarsa decemlineata microsatellite loci isolated using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol is reported. Three to 15 alleles per locus were detected in 54 beetles collected from four populations of L. decemlineata. The mean number of alleles was 7.4 ± 3.2 and the level of expected heterozygosity ranged from 0.451 to 0.798. The total exclusionary probabilities using these loci for the first and the second parent were 0.982 and 0.999, respectively. These are the first microsatellite loci characterized from the Colorado potato beetles that can be used for estimating genetic diversity, population structure and parentage analysis.     

Genetic diversity and bottleneck studies in the Marwari horse breed

Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (±s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, F_IS (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significantM ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.     

Genetic diversity of the cultured giant freshwater prawn (Macrobrachium rosenbergii) in China based on microsatellite markers

The Giant freshwater prawn (GFP), Macrobrachium rosenbergii, is one of the most important crustacean species cultured in China, but information on the genetic diversity of GFP in China is still limited. In this study we analyzed the genetic diversity of 6 cultured GFP populations collected in China, and 2 wild populations from Viet Nam. The wild populations were included as a reference so that the genetic diversity of the introduced cultured GFP populations could be evaluated. We used six polymorphic primer pairs to estimate genetic diversity. Results showed that the number of alleles per locus ranged from 6 to 19. The mean observed heterozygosity (0.364 ± 0.090) was less than the expected heterozygosity (0.893 ± 0.016); highly significant deficiencies in heterozygotes were detected (100%). The polymorphism information content (PIC) of 8 populations at 6 loci was greater than 0.5 (varying from 0.616 to 0.912). Pair-wise genetic differentiation (F_ST) varied from 0.006 to 0.129 among the eight populations. The dendrogram based on genetic distance showed six populations distributed on the same major branch, suggesting that they have closely genetic distance and two populations (ZJC and GDB) distributed on the other branch, so they also have closely genetic distance. The results of study provide a baseline assessment of genetic diversity in some populations in China and Viet Nam that will be useful for the development of breeding programmes in the future.     

Genetic diversity of castor bean (Ricinus communis L.) in Northeast China revealed by ISSR markers

Inter-Simple Sequence Repeat (ISSR) markers were employed to analyze the genetic diversity of Ricinus communis L. in northeastern China plants. We selected ten primers that produced clear, reproducible and multiple bands for these experiments and 179 bands were obtained across 39 genotypes. Polymorphic band ratios ranged from 100% to a minimum of 78.9% with an average of 96.4% while band numbers were comprised between 13 (UBC823) and 23 (UBC856). The results obtained from UPGMA clustering dendrogram and PCoA lead to 39 distinct castor bean accessions belonging to four major groups. We found that all groups shared a common node with 66% similarity while Jaccard's similarity coefficient ranged from 0.58 to 0.92. Compatible inference was also observed from the high values of heterozygosity (Ht = 0.3378 ± 0.0218), Nei's genetic diversity (H = 0.1765 ± 0.2090), and Shannon's information index (I = 0.4942 ± 0.1872). In addition, our data reveal a Nei's genetic differentiation index (G_ST) of 0.3452 and estimated the gene flow (Nm) at 0.9482. These findings clearly suggest a genetic diversity in castor bean germplasms from various geographic origins and contribute to our understanding of breeding and conservation of castor beans.     

Variation of 18 STR loci in Shahabadi sheep of India

Shahabadi sheep represent an important but uninvestigated source of genetic diversity. Eighteen microsatellite markers were employed to analyze the genetic diversity of Shahabadi sheep population found in Bihar, India within fifty samples. Microsatellites were highly polymorphic with a mean allelic number 5.56 ± 1.79. The observed heterozygosity, expected heterozygosity and observed and effective number of alleles were used to estimate the genetic variation of this breed. The observed heterozygosity in the population varied from 0.279–0.739 with the mean of 0.501 ± 0.151, reflecting substantial genetic variation in this population. Population was observed to be heterozygote deficient (21.5%). The results of this study indicated that conservation of genetic variation in Shahabadi population should be considered by breeders, in the interest of long term future of the breed in its native tract.     

Isolation and characterization of twelve polymorphic microsatellite markers for the invasive ascidian Styela clava (Tunicata)

The invasive solitary ascidian Styela clava has spread extensively along European coasts since its first occurrence in the early 1950s. In order to characterize spatial and temporal patterns of genetic change during its establishment and subsequent spread, we developed 12 species‐specific loci from an enriched microsatellite library. Polymorphism was explored in one native and two introduced populations (N = 31 ± 1). Number of alleles per locus varied from two to 13 (mean = 7). The average expected heterozygosity within populations ranged from 0.539 to 0.580.     

Characterization of eight polymorphic microsatellite markers in the tarnished plant bug,Lygus lineolaris (Palisot de Beauvois)

A partial genomic library of the tarnished plant bug, Lygus lineolaris, enriched for microsatellite sequences was screened to identify marker loci. Eight polymorphic loci suitable for population genetic studies were identified by screening 192 field‐collected insects. The observed number of alleles ranged from four to 21 with an average of 12.25 (SE ± 1.94) while the effective number of alleles ranged from 1.23 to 11.05 with an average of 4.49 (SE ± 1.15). No linkage disequilibria or significant deviations from Hardy–Weinberg expectations were detected at any of the loci. Seven of the eight L. lineolaris microsatellite loci were transferable to Lygus hesperus.     

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H_O) and expected (H_E) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f₄ statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.     

Comparative analysis of gonadal morphology in six fish species of the Incertae Sedis genera in Characidae of occurrence in the São Francisco River Basin,Brazil

Martins, Y.S., Arantes, F.P., Sato, Y., dos Santos, J.E., Rizzo, E. and Bazzoli, N. 2012. Comparative analysis of gonadal morphology in six fish species of the Incertae Sedis genera in Characidae of occurrence in the São Francisco River Basin, Brazil. —Acta Zoologica (Stockholm) 93 : 48–56. This study presents a comparative analysis aiming to show the remarkable differences found in gonad morphology between six fish species from the genera Incertae Sedis in the Characidae family. Maturing ovaries of Astyanax fasciatus presented grayish color whilst the other species’ were yellowish in color. The cortical alveoli of the analyzed species are small (5.20 ± 1.44–8.28 ± 2.02 μm) and are formed by various discontinuous layers of vesicles except in the Bryconops affinis, where they are large (12.87 ± 2.41 μm) and form various continuous layers of vesicles. The pellucid zone is thin and varies from 2.44 ± 0.90 to 5.79 ± 1.90 μm and is thickest in B. affinis (10.57 ± 2.08 μm). Folds in the pellucid zone were observed in Astyanax bimaculatus, A. fasciatus, Hemigrammus marginatus, and Moenkhausia costae. The follicular cells of B. affinis are columnar (28.19 ± 13.71 μm), while they are squamous in other species (1.52 ± 0.64–2.12 ± 0.78 μm). This study showed that the morphologic and biometric characteristics of the B. affinis vitellogenic oocytes are statistically different than the analyzed other ones Incertae Sedis of the Characidae family. In advanced maturing testis of A. bimaculatus and A. fasciatus, the spermatozoa were embedded in acidophilic secretion which was gradually reabsorbed in the seminiferous tubules when males were partially spent.     

Genetic divergence between populations of two closely related troglobitic beetle species (Speonomus: Bathysciinae,Coleoptera)

Genetic variability and divergence at 13 enzyme loci were studied in two species of troglobitic beetles (Speonomus zophosinus andhydrophilus 12 populations) collected from the Pyrenees mountains. These allopatric species exhibit a high degree of specialization to underground life and a very small geographical range. Four diagnostic loci arePgi, Est-2, Pac-1, Phi. Within each species polymorphic loci exhibited marked spatial variation of allele frequencies, sometimes over short distances (5–10 km). The levels of genetic variability are comparable to those observed in non-cave invertebrates (frequency of polymorphic loci: 0.31; average expected heterozygosity: 0.112±0.015). Moreover, a single species showed variability in the average level of heterozygosity (0.06 to 0.172). Patterns of genetic differentiation among species were also studied; mean genetic distance (D: 0.263±0.010) between the twoSpeonomus species was of the same order of magnitude as most data reported in the literature between species. A significant heterozygote deficiency occurs in local populations and for all loci. This deficit does not vary from locus to locus. Several hypotheses were examined in an attempt to account for these observations in connection with the species biology. This deficit probably is due to the breeding structure of the population (inbreeding and assortative mating) coupled with limited dispersal ability.     

Development and polymorphisms of microsatellite markers for hinoki (Chamaecyparis obtusa)

Fifteen microsatellite markers were developed from a microsatellite‐enriched library and characterized using 32 Chamaecyparis obtusa individuals. The number of alleles ranged from two to 27 per locus, with observed heterozygosity ranging from 0.281 to 0.906. The polymorphism information content (PIC) was also calculated for each marker and the average was 0.796 ± 0.024. These microsatellite markers will be useful for investigating population genetics, reproductive ecology, tree improvement and constructing linkage maps of the species.     

Early embryonic development of brackish water Killifish Aphanius hormuzensis (Teleostei,Aphaniidae) inhabiting coastal environment in Southern Iran

The embryonic and early developmental stages of Killifish Aphanius hormuzensis reared in a laboratory condition were investigated in detail using light microscopy. The adult male and female of A. hormuzensis were captured from the wild. They were kept in laboratory condition for 2 months and spontaneously spawned at 28 ± 1°C. The fertilized macrolecithal eggs were characterized with spherical shape, transparent and average 1.60 ± 0.20 mm in diameter. The embryonic development was started with fertilized egg activation and the first cleavage was observed in 2.5 hr ± 20 min post fertilization (hpf), followed by blastula formation and gastrulation stages in 7 and 11 hpf respectively. First somite was observed in 20 hpf and the heart beating was detected in 25 hpf. The early ontogeny of A. hormuzensis was followed by complements of organs formation and the newly hatched larva with 4.9 ± 0.10 mm in length was detected in 166 hpf. This study provides a basis for further research on reproductive biology, conservation and breeding of this species.     

Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers

The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. A wide array of sheep breeds with abundant phenotypic diversity exists including domestication and selection as well as the indigenous breeds may harbor specific features as a result of adaptation to their environment. The objective of this study was to investigate the population structure of indigenous sheep in a large geographic location of the Chinese mainland. Six microsatellites were genotyped for 611 individuals from 14 populations. The mean number of alleles (±SD) ranged from 7.00 ± 3.69 in Gangba sheep to 10.50 ± 4.23 in Tibetan sheep. The observed heterozygote frequency (±SD) within a population ranged from 0.58 ± 0.03 in Gangba sheep to 0.71 ± 0.03 in Zazakh sheep and Minxian black fur sheep. In addition, there was a low pairwise difference among the Minxian black fur sheep, Mongolian sheep, Gansu alpine merino, and Lanzhou fat‐tailed sheep. Bayesian analysis with the program STRUCTURE showed support for 3 clusters, revealing a vague genetic clustering pattern with geographic location. The results of the current study inferred high genetic diversity within these native sheep in the Chinese mainland.     

Genetic variation within and between populations of hermaphroditic <Emphasis Type="Italic">Bulinus truncatus</Emphasis> tetraploid freshwater snails of the Albertine Rift,East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.