Mean Number Of Alleles Research Articles

Assessment of Genetic Diversity in Chokla Sheep Breed of Rajasthan Using Microsatellite Markers

Genetic diversity of Chokla sheep breed was investigated using 18 microsatellite markers suggested by FAO. Total of 150 alleles were detected across 18 microsatellite loci. The highly polymorphic locus was OarFCB48 with 13 alleles and the lowest number of allele was found in FCB128. All the loci were found highly polymorphic with 94% polymorphism in studied population, where mean polymorphic information content value was found 0.751, indicating utility of these markers for genome mapping as well as population assignment. Various diversity estimates, mean observed heterozygosity (0.576), mean number of alleles (8.3), effective number of alleles (5.2) and gene diversity (0.783) showed significant within-breed diversity in studied population. However, positive Fis value (0.256) indicated heterozygote deficiency in investigated sheep population. This study is important to understand the genetic diversity of studied population in present scenario for adjudication of demanded breeding programms as well as for creating useful conservation strategies.

Investigation of Markers of Artemisinin Resistance at Selected Intervals during the 72 h Period after Artemisinin based Combination Therapy Dosing in Kisumu Western Kenya

Background: Microscopic parasite detection during the course of treatment or follow-up suggests that a proportion of ACT treated children in Kenya do not completely clear Plasmodium falciparum parasitemia. Plasmodium falciparum mutation in chloroquine resistance transporter gene (Pfcrt76), multidrug resistance gene1 (Pfmdr1), deubiquitinating enzyme gene (Pfcubp-1) and clathrin vesicle associated adapter 2, u subunit encoding gene (Pfap2mu) and multidrug resistant protein 1 gene (Pfmrp1) have been associated with subsequent patent recrudescence after ACT treatment. As there are no validated markers of ACT resistance in Africa to-date, surveillance of changes in these polymorphisms during the course of treatment is useful in establishing their role in ACT treatment outcome. Methods: 118 P. falciparum 2013 to 2015 samples from ACT clinical efficacy studies were genotyped for frequency of drug resistance polymorphisms using sequence analyzers. Each sample was screened at least three to four-time points namely; day zero before start of treatment then days 2 and 3 after initiation of treatment plus the day of subsequent parasitemia by microscopy prior to day 42 for some of the subjects. Sequence analyzers were used to genotype for frequency of drug resistance polymorphisms, Pfmdr1 gene copy number and genetic diversity typing of the 12 microsatellite loci. Genetic diversity of parasite populations across four time-points was determined by analysis of 12 microsatellite loci. Worldwide Antimalarial Resistance Network’s parasite clearance estimator (PCE) was used to determine parasite clearance rates. Results: The new genes Pfap2mu and Pfubp had S145C and E1528D being most polymorphic with prevalence’s of 18% and 19%, respectively Pfmdr1 86,184 and 1246 had significant increase in wild type alleles between day zero and time-points 3 and 4. Microsatellite profile analysis show that the mean number of alleles in all the loci across the 8 populations ranged from 9.250 to 1.000. Poly α was the most polymorphic with 35 alleles. The mean unbiased HE was 0.672 while Shannon diversity index for the 8 populations was ranging between 0.182-0.000, none of the parasite analyzed had matching haplotypes. The mean parasite clearance half-life was 2.63 h (95% confidence interval [CI]) and the median clearance half-life was 2.24 h. The parasite clearance half-life ranged from 1.14-5.05 h. Conclusion: Increased wild-type Pfmdr1 86,184 and 1246 as well as polymorphisms in Pfap2mu and Pfcubp-1 in post day zero suggest that these genes could be responding to ACT dosing and therefore require continued monitoring. Samples with multiple copies of the Pfmdr1 did not indicate show effect on parasite clearance rate. Though there was no correlation between these profiles and clearance rates, further evaluations are needed to determine the potential public health implications of these observations and the utility of these loci as markers of artemisinin sensitivity in populations of P. falciparum worldwide.

A mountain range is a strong genetic barrier between populations of Afzelia quanzensis (pod mahogany) with low genetic diversity

Understanding patterns of genetic diversity of plants is important in guiding conservation programs. The aim of our study was to characterize genetic diversity in Afzelia quanzensis, an economically important African tree species. We genotyped 192 individuals at 10 nuclear microsatellite loci. Samples were collected from nine sites in Zimbabwe, five in the north and four in the south, separated by a mountain range, the Kalahari-Zimbabwe axis. Overall, genetic diversity was relatively low across all sites (expected heterozygosity (H E) = 0.452, mean number of alleles (A) = 4.367, allelic richness (A R) = 2.917, effective number of alleles (A E) = 2.208, and private allelic richness (PAR) = 0.197). Genetic diversity estimates, H E, A, A R, and PAR, were not significantly different between northern and southern sites. Allelic richness was significantly higher in southern sites. Significant population differentiation was observed among all sites (F ST = 0.0936, G′ ST = 0.1982, G ST = 0.1001, D JOST = 0.0598). STRUCTURE analysis and principal components analysis identified two gene pools, one predominantly made up of southern individuals, and the other of northern individuals. A Monmonier’s function detected a genetic barrier that coincided with the Kalahari-Zimbabwe axis. The relatively low level of genetic diversity in A. quanzensis may reduce adaptability and limit future evolutionary responses. All sites should be monitored for deleterious effects of low genetic diversity, and genetic resource management should take into consideration the existence of the distinct gene pools to capture the entire extant genetic variation.

Genetic tracing of farmed shrimp (Decapoda, Penaeidae) in wild populations from a main aquaculture region in Mexico

Release or escapes of aquaculture organisms may impact the genetic composition and variability of wild populations, leading to diverse issues that may compromise long-term wild stock fitness. Therefore, it is relevant to determine if farmed stocks are currently interacting with wild populations. Shrimp farming is an aquaculture activity taking place along the tropical Pacific coast of the Americas, and represents the most important culture bussiness of Northwestern Mexico. In this study, wild and farmed whiteleg shrimp Litopenaeus vannamei from the State of Sinaloa were genetically evaluated to determine admixture levels. A newly developed set of 14 microsatellite markers (mean number of alleles per locus 11.8, and 0.836 expected heterozygosity) was obtained by Next Generation Sequencing to characterize samples. Sampling consisted of 32 wild shrimps collected during three years (2002, 2012, and 2013) and three different sites, and two hatchery stocks from 2007. No significant differences were observed among years in the wild samples, but cluster analyses showed that hatchery-produced individuals were different from wild specimens. Deviations from Hardy-Weinberg Equilibrium and genotype assignment tests indicated that a fraction from each sample could contain individuals from hatchery origin. Even though the estimated fraction of escaped farmed individuals in the most recent samples (2012-2013; mean = 7.1 %) is considered of low genetic risk, management recommendations for hatcheries and farms were provided. Besides, the reasons that explain the intended and unintended farmed shrimp release into the wild were discussed.

Microsatellite analysis of genetic diversity and population structure of hermaphrodite ridge gourd (Luffa hermaphrodita).

Out of 103 microsatellite markers used for studying the genetic diversity among local landraces of Luffa species, 56 were found polymorphic, including 38 gSSR and 18 eSSR, respectively. A total of 197 amplification products were obtained. The mean number of alleles per locus was 3.52. The PIC ranged from 0.037 to 0.986, while size of amplified product ranged from 105 to 500bp. Cucumber-derived SSRs were amplified within L. acutangula (68%), L. aegyptiaca (61.16%), and L. hermaphrodita (60.2%), with an average of 63.12% cross-transferability. The Jaccard's coefficient ranged from 0.66 to 0.97, with an average of 0.81. High genetic variability was observed for node of 1st hermaphrodite flower (6.4-17), days to 1st hermaphrodite flower (38-52.1), days to 1st fruit harvest (43-65), number of fruit per cluster (1-5.9), fruit length (3.9-25cm), fruit weight (18.4-175g), number of fruit per plant (20-147.5), and yield per plant (2.2-4.7kg). Two sub-populations were identified including 21 genotypes (sub-population I) and 06 genotypes (sub-population II), these two sub-populations showed 0.608-0.395% of the ancestral relationship to each other. This study provides information for future exploration, collection, and utilization of Luffa genotypes, as well as the polymorphic markers identified could be available for the study of landmarks in linkages, genomic structures, evolutionary ecology, and marker-assisted selection (MAS) in Luffa species.

Genetic characterization of the Crataegus genus: Implications for in situ conservation

Abstract Iran is remarkably rich in the genus Crataegus. Hawthorns can be used as a rootstock for pear and quince. The objective of the present study was to obtain an overview on the genetic relatedness among and within 201 accessions of genus Crataegus in Iran using three types of molecular markers. A total of 13 ISSR and 13 SCoT primers were used which produced 130 and 132 amplified fragments, of which 116 (88.94%) and 115 (86.54%) bands were polymorphic. Also, the total number of amplified alleles by 11 SSR primer pairs was 76 and the mean number of alleles per locus (Na) ranged from 3.81 to 5.44, while the mean number of effective alleles per locus (Ne) varied from 2.83 to 3.86. Genetic similarity (GS) by Jaccard’s similarity coefficient ranged 0.23–0.70 by ISSR, 0.02–0.62 by SCoT and 0.00–0.85 by SSR, indicating a high level of genetic variation that exists in the studied gene pool. The UPGMA dendrograms and Bayesian clustering analysis constructed based on all of the three molecular systems separated the genotypes into three main clusters with several sub-clusters indicating considerable genetic diversity in the studied germplasm. The information obtained here could be valuable for devising strategies for the germplasm conservation.

Characterization of 27 novel microsatellite loci in Sinibotia superciliaris (Günther 1892) and cross-species transferability in Sinibotia reevesae (Chang 1944)

The Chinese golden loach, Sinibotia superciliaris and its congener Sinibotia reevesae, are endemic to China and extraordinary similar in morphological traits. However, few genetic studies have been conducted on them, especially those based on nuclear markers. Here, we developed 27 novel polymorphic microsatellite markers from S. superciliaris and further tested the cross-species transferability of those loci in S. reevesae. The cross-species amplification test showed that 19 loci demonstrate polymorphism in S. reevesae. The mean number of alleles (NA) were both 3 in S. superciliaris and S. reevesae, the mean expected heterozygosities (HE) were 0.57 and 0.54, the Shannon-Wiener Diversity Indices (SW) were 0.84 and 0.82, and the evenness (E) were 0.09 and 0.08, respectively. The polymorphic information content (PIC) showed a high level of polymorphism for the two species (mean 0.54 and 0.50, respectively). In addition, the cross-species transferability (100%) of those markers was clearly high, which confirmed that the microsatellite markers developed here could be used effectively for other related species.

Development of microsatellite markers for the endangered semi‐shrub Chimaphila umbellata (Ericaceae)

AbstractBased on the DNA sequencing reads obtained using 454 pyrosequencing, primers amplifying 16 microsatellite loci were developed for the endangered semi‐shrub Chimaphila umbellata, which occurs sporadically in the Japanese Archipelago. These 16 loci were polymorphic in the populations sampled from the Hokkaido and Tohoku Districts; the mean number of alleles was 3.31 and 3.44, and the mean expected heterozygosity was 0.42 and 0.44, respectively. These loci were not linked to each other and contained no null alleles. Amplification using these primers was also tested in the congeneric species C. japonica, but only three of them successfully amplified DNA of the species. These markers will be used to examine genetic diversity and genetic differentiation in populations of C. umbellata.

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

AbstractCarniolan honeybee (

Genetic diversity of Afrikaner cattle in southern Africa.

The Afrikaner is an indigenous South African breed of "Sanga" type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.

Development and characterization of genomic SSR markers for Anneslea fragrans (Pentaphylacaceae).

Premise of the study:The genus Anneslea (Pentaphylacaceae) contains four species and six varieties, most of which are locally endemic. Here, simple sequence repeat (SSR) markers were developed for the conservation of these species.Methods and Results:The genome of A. fragrans was sequenced and de novo assembled into 445,162 contigs, of which 30,409 SSR loci were detected. Primers for 100 SSR loci were validated with PCR amplification in three populations of A. fragrans. Seventy-nine loci successfully amplified, and 30 were polymorphic. The mean number of alleles, observed heterozygosity, and expected heterozygosity were 7.01 ± 1.60, 0.817 ± 0.241, and 0.796 ± 0.145, respectively. Most primers could be amplified in Ternstroemia gymnanthera, T. kwangtungensis, and Cleyera pachyphylla.Conclusions:Our study demonstrated that shotgun genome sequencing is an efficient way to develop genomic SSR markers for nonmodel species. These genomic SSR loci will be valuable in population genetic studies in Anneslea and its relatives.

Phenotypic and genetic characterization of the Italian bantam chicken breed Mericanel della Brianza

Abstract The development of the large-scale intensive poultry production system caused, in recent past, an almost complete disappearance of native breeds. The Mericanel della Brianza (MB) is an Italian bantam chicken breed characterized by optimal rusticity and a very good attitude to broodiness. The aim of this study was to assess peculiar phenotypic characteristics, breeding performance and genetic makeup of a small MB chicken nucleus under an in situ conservation program at the Poultry Conservation Centre of Local Genetic Resources of the University of Milan since 2010. The number of selected breeders in the nucleus progressively increased over the 5 years time from 22 (8M+14F) in 2010 to 58 (10M+48F) in 2014. FAO guidelines for phenotypic characterization of animal genetic resources were used to describe the productive, the reproductive traits and the performance of the MB chickens. The mean number of eggs per hen per week increased progressively from 1.86 in 2010 to 2.33 in 2014. Overall mean egg weight was 33.8 g (SD 3.71 g and CV 11%) and proportion of fertile eggs was 84%. Genetic screening of breeders was performed in 2010, 2012 and 2014 using the panel of 30 microsatellite loci recommended by ISAG and FAO for biodiversity studies. A total of 120 blood samples from twenty-four families (eight in 2010, six in 2012 and ten in 2014) were included in the study. The Mean Number of Alleles (MNA), the allelic frequencies, the observed (H O ) and expected (H E ) heterozygosity, the Polymorphism Information Content (PIC) and the inbreeding coefficient (F IS ) value were estimated. All markers were polymorphic with the exception of the MCW0034 and MCW0248 loci. These two markers and other 4, not properly amplifying, were excluded from analyses. A total number of 77 alleles (MNA = 3.08) in 25 microsatellites have been detected in the overall population. The genetic diversity within and among families was determined with the Wright's F-statistics fixation index (F ST ). F ST showed similarities among breeders within the nucleus in 2012 and 2014, but disclosed a variation respect to the nucleus of individuals of 2010. The genetic distance observed across years was confirmed by the PCA analysis. Despite the selection applied to decrease the presence of undesired traits (i.e. both morphological and reproductive traits), the genetic variability was conserved in the nucleus population across years.

Estimation of genetic diversity and relationship among goats of Maharashtra state

Sangamneri, Osmanabadi, Berari and Konkan Kanyal are the known breeds of Maharashtra state of India. DNA from 50 unrelated goats of each breed was analysed to know the genetic diversity using 25 microsatellite markers. A total of 479 alleles (192 in Sangamneri, 153 in Osmanabadi, 294 in Berari and 255 in Konkan Kanyal) were observed. Mean number of alleles per locus and observed heterozygosity were 7.68, 6.12, 11.76, 10.20 and 0.53, 0.42, 0.67 and 0.58 for Sangamneri, Osmanabadi, Berari and Kanyal goat populations respectively. The fixation coefficients of sub-populations within the total population (FST), varied from 0.04 (OarHH64) to 0.68 (OarJMP29) with a mean of 0.17. The L-shaped mode-shift curve indicated the absence of reduction in effective population size. The genetic distances between four breeds indicated the distinctness of Berari and Konkan Kanyal from Sangamneri and Osmanabadi. Berari and Konkan Kanyal although exists at different geographic locations but show some genetic overlapping. The Nei's genetic distance observed between breeds were 0.472 (Sangamneri and Osmanabadi), 0.667 (Sangamneri and Berari), 0.819 (Sangamneri and Konkan Kanyal), 0.797(Osmanabadi and Berari), 0.994 (Osmanabadi and Konkan Kanyal) and 0.092 (Berari and Konkan Kanyal). Konkan Kanyal is genetically more distant from Osmanabadi and Sangamneri than Berari. Sangamneri and Osmanabadi goat breeds were assigned to cluster-3 where the proportion of membership for each breed was 0.975 (Sangamneri) and 0.992 (Osmanabadi). Kanyal and Berari goat populations were assigned to another cluster (Cluster 4). The proportion for their membership was 0.923 (Konkan Kanyal) and 0.869 (Berari).

Development and characterization of the first 16 microsatellites loci for Panulirus pascuensis (Decapoda: Palinuridae) from Easter Island using Next Generation Sequencing

The spiny lobster Panulirus pascuensis stands out among the endemic species of Easter Island, due to its cultural and economic importance. A total of 16 microsatellite loci were characterized in 18 individuals, 9 of which were polymorphic. The mean number of alleles per locus was 3.44 (2-6) and the observed heterozygosity ranged from 0.11 to 0.93. None of the loci exhibited significant linkage disequilibrium or departures from HWE. These new microsatellites will be used to obtain information about migration, population structure and genetic diversity of P. pascuensis in order to improve the future sustainable management and conservation plans.

Genetic structure and gene flow of the flea Xenopsylla cheopis in Madagascar and Mayotte

BackgroundThe flea Xenopsylla cheopis (Siphonaptera: Pulicidae) is a vector of plague. Despite this insect’s medical importance, especially in Madagascar where plague is endemic, little is known about the organization of its natural populations. We undertook population genetic analyses (i) to determine the spatial genetic structure of X. cheopis in Madagascar and (ii) to determine the potential risk of plague introduction in the neighboring island of Mayotte.ResultsWe genotyped 205 fleas from 12 sites using nine microsatellite markers. Madagascan populations of X. cheopis differed, with the mean number of alleles per locus per population ranging from 1.78 to 4.44 and with moderate to high levels of genetic differentiation between populations. Three distinct genetic clusters were identified, with different geographical distributions but with some apparent gene flow between both islands and within Malagasy regions. The approximate Bayesian computation (ABC) used to test the predominant direction of flea dispersal implied a recent population introduction from Mayotte to Madagascar, which was estimated to have occurred between 1993 and 2012. The impact of this flea introduction in terms of plague transmission in Madagascar is unclear, but the low level of flea exchange between the two islands seems to keep Mayotte free of plague for now.ConclusionThis study highlights the occurrence of genetic structure among populations of the flea vector of plague, X. cheopis, in Madagascar and suggests that a flea population from Mayotte has been introduced to Madagascar recently. As plague has not been reported in Mayotte, this introduction is unlikely to present a major concern for plague transmission. Nonetheless, evidence of connectivity among flea populations in the two islands indicates a possibility for dispersal by fleas in the opposite direction and thus a risk of plague introduction to Mayotte.

Genetic variability and phylogenetic relationship establishes distinctness of Kaunayen chicken of Manipur

Conservation of locally adapted indigenous livestock has become an important objective in sustainable animal breeding.The current study is first detailed analysis of the genetic diversity harboured by Kaunayen chicken of Manipur.The genotype data generated on 24 microsatellite markers was analysed to establish distinctness of Kaunayen from other registered poultry breeds of India. Large number of observed alleles (212) and heterozygosity (0.66) indicated high genetic diversity. Mean number of alleles observed in Kaunayen chicken were 8.83±0.31 and ranged between 4 (MCW250 and LEI174) and 15 (LEI120). Mean effective number of alleles was significantly less (4.11±0.38) than the observed number of alleles. The maximum observed heterozygosity (1.0) was observed in MCW262 locus and the minimum (0.368) in LEI166. The expected heterozygosity (0.706) was more than the observed heterozygosity (0.664±0.036) which points to heterozygote deficiency and was also reflected in positive FIS estimate (0.06) for the population. Non-significant heterozygote excess on the basis of Infinite allele model and Two-phase model in conjunction with mode-shift analysis test, indicated an absence of bottleneck. Phylogenetic reconstruction on the basis of genetic distance places Kaunayen chicken as a distinct population with respect to other poultry breeds of India. All analysis showed that a significant amount of genetic variation is maintained in Kaunayen chicken population and has appropriately been registered as the 17th chicken breed of India.

Highly polymorphic microsatellite loci for the Acapulco damselfish, Stegastes acapulcoensis, and cross amplification in three congeneric species

In the present study we report a set of 13 novel microsatellites isolated from and characterized for the Acapulco damselfish Stegastes acapulcoensis, a species endemic to, but widely distributed within, the Eastern Tropical Pacific (ETP) region. The loci were tested in 30 individuals from the Colombian Pacific and were highly polymorphic. The mean allele number per locus was 19.5 (± 4.03 SD) and the observed heterozygosities ranged from 0.192 to 1. Some of the loci were successfully cross-amplified and were polymorphic in three Stegastes species from the ETP: S. arcifrons, S. flavilatus and S. beebei (with 11, three and seven amplified loci, respectively). The high variability and cross-amplification success of the new set of microsatellites reported here allows these markers to be a useful resource for genetic studies of S. acapulcoensis and some of their congeners to address evolutionary, ecological and conservation-related questions in the Eastern Tropical Pacific.

<b>Genetic diversity of the Green Turtle (Testudines: Cheloniidae: <I>Chelonia mydas</I> (Linnaeus, 1758)) population nesting at Kosgoda Rookery, Sri Lanka</b>

We determined the genetic diversity of the Green Turtle Chelonia mydas (Linneaus, 1758) nesting at Kosgoda rookery, the second largest sea turtle aggregation on the southwestern coast of Sri Lanka. Skin tissue samples were collected from 68 nesting females and genetic diversity was estimated using six microsatellite loci. High genetic diversity was observed within the population as all loci analyzed were highly polymorphic with a total of 149 alleles observed. The mean number of alleles per locus was 24.7 and the mean observed and expected heterozygosity across all loci were 0.75 and 0.93, respectively. It appears that five out of six loci were not in Hardy-Weinberg equilibrium, while micro-checker analysis suggested that the Kosgoda Green Turtle population was possibly in equilibrium. The viability of a population is unlikely to be reduced if high genetic diversity is maintained within it. Although the Green Turtle population nesting at Kosgoda is small compared to other nesting rookeries in the world, the high genetic diversity observed suggests that the population may not be undergoing a bottleneck.

Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

A New Set of Nuclear Microsatellites for an Ecologically and Economically Important Conifer: the European Black Pine (Pinus nigra Arn.)

The European black pine (Pinus nigra Arn.) is an ecologically and economically important conifer discontinuously and often patchily distributed across different ecological environments and climatic conditions around the Mediterranean Basin. Many studies aiming at understanding the evolutionary history of the species have been carried out, particularly in the hope of resolving the taxonomy of this collective species where many subspecies have been described. So far, neither morphology, enzyme, and metabolite polymorphism nor DNA marker studies have been able to converge on a single taxonomy, and the evolutionary history of the European black pine remains unclear. To date, nuclear microsatellites (nSSRs) are not available for P. nigra. In this work we designed two multiplexes of eight and six nSSRs each, both characterized by high amplification quality and polymorphism. Nine nSSRs were specifically developed for the European black pine starting from six transcriptomes sequenced using Next Generation Sequencing (NGS) techniques following the Illumina method, while five previously developed for other pines were successfully transferred to P. nigra. The mean number of alleles per locus was 5.9, and the observed heterozygosity ranged between 0.341 and 0.875. F ST was statistically significant for all loci, and Bayesian clustering approaches revealed a geographically meaningful population structure. We thus show this set of 14 nSSRs to be highly informative for population genetic studies and of significant interest to resolve the taxonomy of the European black pine.