Excess Homozygosity Research Articles

Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.

Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis dataset

BackgroundWhen selecting mates, many vertebrate species seek partners with major histocompatibility complex (MHC) genes different from their own, presumably in response to selective pressure against inbreeding and towards MHC diversity. Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions.ResultsUsing a multi-analytical strategy, we report validated genome-wide relationships between genetic identity and human mate choice in 930 couples of European ancestry. We found significant similarity between spouses in the MHC at class I region in chromosome 6p21, and at the odorant receptor family 13 locus in chromosome 9. Conversely, there was significant dissimilarity in the MHC class II region, near the HLA-DQA1 and -DQB1 genes. We also found that genomic regions with significant similarity between spouses show excessive homozygosity in the general population (assessed in the HapMap CEU dataset). Conversely, loci that were significantly dissimilar among spouses were more likely to show excessive heterozygosity in the general population.ConclusionsThis study highlights complex patterns of genomic identity among partners in unrelated couples, consistent with a multi-faceted role for genetic factors in mate choice behavior in human populations.

The origin and genetic variation of domestic chickens with special reference to junglefowls Gallus g. gallus and G. varius.

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

A powerful score test to detect positive selection in genome-wide scans.

One of the surest signatures of recent positive selection is a local elevation of advantageous allele frequency and linkage disequilibrium (LD). We proposed to detect such hitchhiking effects by using extended stretches of homozygosity as a surrogate indicator of recent positive selection. An extended haplotype-based homozygosity score test (EHHST) was developed to detect excess homozygosity. The EHHST conditioned on existing LD and it tested the haplotype version of the Hardy-Weinberg equilibrium. Compared with existing popular tests, which usually lack clear distribution, the EHHST is asymptotically normal, which makes analysis and applications easier. In particular, the EHHST facilitates the computation of an asymptotic P-value instead of an empirical P-value, using simulations. We evaluated by simulation that the EHHST led to appropriate false-positive rates, and it had higher or similar power as the existing popular methods. The method was applied to HapMap Phase II data. We were able to replicate previous findings of strong positive selection in 17 autosome genomic regions out of 20 reported candidates. On the basis of high EHHST values and population differentiations, we identified 15 new candidate regions that could undergo recent selection.

Genetic structure of Pinus pinaster Ait. populations in Morocco revealed by nuclear microsatellites

Pinus pinaster is one of the most popular conifers used for reforestation in Morocco and represents an economically and ecologically important species for the region. In this study, nuclear microsatellites (ncSSRs) are used to compare genetic structure and diversity estimates of natural populations of Moroccan maritime pine. Samples were collected among 10 natural populations distributed in three biogeographically different regions, the Rif Mountain, the Middle and the High Atlas. Forty-five nuclear alleles at seven variable loci were found with a mean of 6.4 alleles per locus. A number of private alleles (17.1%) were shown in populations from Rif and Middle Atlas. Moreover, in Morocco, P. pinaster showed a lower genetic diversity than in other parts of its geographic range. Significant departures from Hardy–Weinberg equilibrium with excess homozygosity are observed indicating a high level of mating inside populations. Genetic diversity was structured with high variability among populations (Fst = 12%). Results show a correlation between genetic and geographic distances with an R-squared of 0.436. Two clusters were found using STRUCTURE, whereas three main clusters can be distinguished based on genetic distances of phylogenetic tree. Genetic relationships among maritime pine populations in Morocco appear to be related to historical, ecological as well as anthropogenic factors, suggesting the need for conservation strategies at the population level.

Skew in the human caveolin 1 gene upstream purine complex homozygote haplotype compartment in multiple sclerosis

Caveolin 1 (CAV1) is a component of the myelin sheath and the expression of the gene encoding this protein is increased during myelination in Schwann cells and oligodendrocytes. We sought to investigate the homozygote haplotype compartment in a recently identified polymorphic purine complex at the upstream region of the human CAV1 gene in multiple sclerosis (MS). In a case/control study design, the region was characterized in 126 cases of MS diagnosed based on the Revised McDonald diagnostic criteria, and 460 controls. We report a skew in the homozygote haplotype compartment in the cases versus controls both in a qualitative and quantitative respect. Excess homozygosity for haplotypes was observed in the MS cases (corrected p < 0.012, OR = 2.54, CI 1.14–5.64). Furthermore, we observed eight homozygote haplotypes in the MS cases that were non-existent in the controls ( p < 0.0003, OR = 20.27, CI 2.50–163.8). For the first time, our data highlight the CAV1 upstream purine complex as a novel susceptibility genomic locus in the pathophysiology of MS. Of utmost importance, the region has been conserved across species, including mouse, guinea pig, rhesus macaque, and human. The functional effect of this region remains to be clarified in the future studies.

Common body mass index-associated variants confer risk of extreme obesity

To investigate the genetic architecture of severe obesity, we performed a genome-wide association study of 775 cases and 3197 unascertained controls at approximately 550,000 markers across the autosomal genome. We found convincing association to the previously described locus including the FTO gene. We also found evidence of association at a further six of 12 other loci previously reported to influence body mass index (BMI) in the general population and one of three associations to severe childhood and adult obesity and that cases have a higher proportion of risk-conferring alleles than controls. We found no evidence of homozygosity at any locus due to identity-by-descent associating with phenotype which would be indicative of rare, penetrant alleles, nor was there excess genome-wide homozygosity in cases relative to controls. Our results suggest that variants influencing BMI also contribute to severe obesity, a condition at the extreme of the phenotypic spectrum rather than a distinct condition.

Mate availability contributes to maintain the mixed‐mating system in a scolytid beetle

We investigated the mating system and population genetic structure of the beetle, Coccotrypes dactyliperda, with life history characteristics that suggest the presence of a stable mixed-mating system. We examined the genetic structure of seven populations in Israel and found significant departures from the Hardy-Weinberg equilibrium and an excess of homozygosity. Inbreeding coefficients were highly variable across populations, suggesting that low levels of outbreeding occur in nature. Experiments were conducted to determine whether the observed high inbreeding in these populations is the result of a reproductive assurance strategy. Females reared in the laboratory took longer to mate with males from the same population (inbreeding) than with males from a different population (outbreeding). These results suggest that females delayed inbreeding, and were more inclined to outbreed when possible. Thus inbreeding, which predominates in most populations, may be due to a shortage of mates for outbreeding rather than a preference for inbreeding. We conclude that C. dactyliperda has a mixed-mating system that may be maintained by a reproductive assurance strategy.

Population Viability Analysis and Genetic Diversity of the Endangered Red DeerCervus elaphusPopulation from Mesola, Italy

The Mesola red deerCervus elaphusin the Po delta are the only native red deer population on the Italian mainland and have been the focus of conservationists and wildlife biologists for some time. In our study, we present a genetic analysis of 25 Mesola red deer on the basis of 20 polymorphic microsatellite loci, aiming at estimating the population's genetic diversity and at providing information for a future genetic screening. In addition, we carried out a population viability analysis (PVA) with demographic and life‐history data available from a long‐term population survey, simulating different management scenarios. Genetic diversity was very low compared to the rest of Europe (observed and expected heterozygosity 0.50 and 0.61, respectively), and an overall excess of homozygosity was indicative of inbreeding. Calculations of the probability of identity and genotype mismatch frequencies suggested that between five and seven highly informative loci were sufficient to resolve individuals with reasonable certainty. The PVA yielded a generally poor outlook, but at the same time, it showed that management measures already taken significantly increased population viability. A sensitivity analysis revealed that inbreeding depression and possible catastrophes had a huge impact on the population's prospects. However, the establishment of two subpopulations and successful attempts at reducing the consequences of catastrophic events were able to significantly mitigate the harmful effects of both inbreeding and environmental stochasticity. These results, in particular the splitting of the population, may be of general interest to conservationists dealing with unique threatened populations.

Development and characterization of novel microsatellite markers isolated from Potentilla fruticosa L. (Rosaceae), and cross-species amplification in its sister species—Potentilla glabra L.

Here, we report development and characterization of 11 new polymorphic microsatellite loci isolated from the genome of Potentilla fruticosa L. (Rosaceae). Polymorphisms of each locus were screened in 12–15 individuals from geographically separated populations. The number of alleles per locus ranged from five to eleven. The observed and expected heterozygosity ranged from 0.22 to 0.35 and 0.38 to 0.53, respectively. These eleven loci were also surveyed for 11 individuals from its sister species, Potentilla glabra L. (Rosaceae). Ten of them were successfully amplified and allelic diversities were also highly polymorphic. Seven loci totally in both species exhibited significant departure from Hardy–Weinberg equilibrium probably due to excessive homozygosity and the population structure within samples. No linkage disequilibrium was detected among all paired loci comparisons. These results demonstrate that these microsatellite markers can be used to characterise the intra- and inter-specific genetic diversity, and will be useful to study the population genetics and speciation history of the two closely related shrubs.

Genome-scale multilocus microsatellite typing of Trypanosoma cruzi discrete typing unit I reveals phylogeographic structure and specific genotypes linked to human infection.

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is “hidden” at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed.

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p<0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so.

Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners

Eight new microsatellite loci were characterized for Littorina saxatilis (Olivi, 1792) and tested for their cross-hybridization in congeners. All loci were polymorphic in Irish and Celtic Sea samples, with an average number of alleles per locus of 15 (range, 6–31). Observed and expected locus heterozygosities ranged from 26 to 85% and from 53 to 92%, respectively. Three loci showed excess homozygosity and significant departures from Hardy–Weinberg expectations in one sample, possibly due to null alleles, population structuring or inbreeding. No linkage disequilibrium was detected among loci within samples. A high degree of cross-hybridization was observed in closely related congeners and most loci were polymorphic. These markers will be useful for investigating population genetic diversity and connectivity in coastal populations, especially for marine reserve design.

Supportive Evidence for Reduced Expression of GNB1L in Schizophrenia

Chromosome 22q11 deletion syndrome (22q11DS) increases the risk of development of schizophrenia more than 10 times compared with that of the general population, indicating that haploinsufficiency of a subset of the more than 20 genes contained in the 22q11DS region could increase the risk of schizophrenia. In the present study, we screened for genes located in the 22q11DS region that are expressed at lower levels in postmortem prefrontal cortex of patients with schizophrenia than in those of controls. Gene expression was screened by Illumina Human-6 Expression BeadChip arrays and confirmed by real-time reverse transcription-polymerase chain reaction assays and Western blot analysis. Expression of GNB1L was lower in patients with schizophrenia than in control subjects in both Australian (10 schizophrenia cases and 10 controls) and Japanese (43 schizophrenia cases and 11 controls) brain samples. TBX1 could not be evaluated due to its low expression levels. Expression levels of the other genes were not significantly lower in patients with schizophrenia than in control subjects. Association analysis of tag single-nucleotide polymorphisms in the GNB1L gene region did not confirm excess homozygosity in 1918 Japanese schizophrenia cases and 1909 Japanese controls. Haloperidol treatment for 50 weeks increased Gnb1l gene expression in prefrontal cortex of mice. Taken together with the impaired prepulse inhibition observed in heterozygous Gnb1l knockout mice reported by the previous study, the present findings support assertions that GNB1L is one of the genes in the 22q11DS region responsible for increasing the risk of schizophrenia.

Characterization of microsatellite markers for snouted treefrogs in the Scinax perpusillus species group (Anura, Hylidae)

We characterized eight microsatellite loci for snouted treefrogs in the Scinax perpusillus species group, a group of hylid frogs endemic to the Atlantic Coastal Forest of Brazil, and tested their utility in mainland and island species of the complex. All eight loci were polymorphic in one population of S. perpusillus; four of the loci showed excess homozygosity and three of those deviated from Hardy–Weinberg expectations, possibly due to null alleles, inbreeding, or population structure in sampled individuals. Six loci amplified and were polymorphic in S. arduous, S. argyreornatus, and S. faivovichi, but only one in S. alcatraz. These markers will be useful for quantifying effects of habitat fragmentation on population genetic diversity and connectivity in coastal and island populations of this threatened species group.

Isolation and characterization of microsatellite markers for Cycas debaoensis Y. C. Zhong et C. J. Chen (Cycadaceae)

Cycas debaoensis is one of the critically endangered cycad species endemic to China. In this study, we described the development of six microsatellite markers from the genome of C. debaoensis using the protocol of fast isolation by AFLP of sequences containing repeats (FIASCO) and two microsatellite markers derived from the database of expressed sequence tags (dbEST). Polymorphism of each locus was assessed in 60 adult individuals of the cycad. The average allele number of the microsatellites was 2.6 per locus, ranging from two to five. The observed and expected heterozygosities varied from 0.0833 to 0.7333 and from 0.0805 to 0.7188, respectively. Despite its rarity, only one locus (Y177) deviated from Hardy-Weinberg equilibrium due to the excessive homozygosity. The marker transferability of the eight primer pairs was tested on other four congeneric species that also occur in China.

Limitations of Genetic Findings That Are Not in Hardy-Weinberg Equilibrium

We thank Drs. Body and Schwinn for their critical remarks on our study.1To clarify, our double-blinded, placebo-controlled trial was primarily designed to test the hypothesis that the perioperative administration of bisoprolol would reduce the incidence of cardiovascular complications in patients with or at risk for coronary artery disease undergoing surgery with spinal nerve block. However, because single nucleotide polymorphisms of the β-adrenergic receptor genes may act as disease modifiers,2biologically important nonsynonymous coding variants of the β-adrenergic receptor were determined in our study population. This analysis showed that carriers of at least one Gly allele of the β1-adrenergic receptor polymorphism Arg389Gly experienced a higher number of adverse events than Arg homozygotes.1Drs. Body and Schwinn raised concerns with respect to genotyping errors based on the observed deviation from Hardy-Weinberg equilibrium for this particular polymorphism in our trial. Genotyping error is indeed one of the many possible sources of Hardy-Weinberg disequilibrium. To exclude this possibility in our trial, we have carefully regenotyped all patients for the Arg389Gly polymorphism using internal controls for wild-type, heterozygous, and mutant genotypes for each amplification process. As reported in our publication, from the 189 patients, who consented to genotyping, 186 could be unequivocally identified and confirmed by regenotyping by three independent individuals. In three patients (notably without a primary outcome), genotyping was not possible, and these patients were excluded from genotype-related outcome analysis. Our genotyping platform was further meticulously validated by bidirectional sequencing of DNA samples for the Arg389Gly polymorphism from 12 randomly selected patients of this particular study and from many other patients not related to this study. Bidirectional sequencing is regarded as the standard of genotyping and as by far more reliable than any other genotyping platform.Although testing for Hardy-Weinberg equilibrium is used as some quality-control measure, particularly in case–control gene association studies, it cannot be used to detect genotyping error.3,4Genotyping errors are generally small and do not generate sufficient deviations from Hardy-Weinberg equilibrium to be detected. In the case of a reduced number of observed heterozygous patients, as may occur in the presence of poor amplification of one of the alleles, large samples sizes are necessary to detect deviations from Hardy-Weinberg equilibrium. For example, with the Gly389 allele of the Arg389Gly polymorphism with a reported allele frequency of 0.27 and an error rate of 0.05, more than 8,000 patients would be necessary to detect deviation from Hardy-Weinberg with a power of 0.80 at an α level of 0.05. Increasing the error rate to 0.15 reduces the sample size to the still considerably high patient number of 944. Therefore, testing for Hardy-Weinberg equilibrium is an unreliable tool to identify genotyping errors. Conversely, the presence of Hardy-Weinberg equilibrium does not rule out that genotyping errors might have occurred. Hence, it seems unlikely that genotyping error is the source of the Hardy-Weinberg disequilibrium observed in our study. Because approximately 10% of all genotype–phenotype association studies show deviation from Hardy-Weinberg equilibrium, the results of our trial cannot be considered “abnormal.”5Rather, as outlined in the discussion of our findings,1a selection bias (population stratification) may have occurred because of inclusion and exclusion criteria of this randomized trial. A mortality bias (different survival of marker genes) due to varying genetic and environmental background (e.g. , response to cardiovascular medication) in this elderly study population at the end of life expectancy may have also caused this disequilibrium. Of note, Hardy-Weinberg disequilibrium that is caused by most interesting biologic phenomena typically results in excess homozygosity, as observed in our study.1However, we agree with Drs. Body and Schwinn that violation of Hardy-Weinberg equilibrium in our study population implies a selected rather than a random sample, invalidating direct comparisons with other populations. Therefore, we share their view that our results should be regarded with caution. Our findings should be confirmed in future prospective larger-scale clinical trials, specifically designed and adequately powered to detect genotype-specific differences in cardiovascular outcome in patients with or at risk of coronary artery disease.*University Hospital Zurich, Zurich, Switzerland. michael.zaugg@usz.ch

Fine‐Scale Population Structure of Rainbow Trout in the Spokane River Drainage in Relation to Hatchery Stocking and Barriers

AbstractWe used 13 microsatellite loci to examine population structure in rainbow trout Oncorhynchus mykiss collected from 20 tributaries and 3 main stems in the greater Spokane River drainage. Populations displayed some excess homozygosity and linkage disequilibrium, which was more pronounced in upper tributary collections and probably the result of small effective population sizes or structuring within tributaries. In general, population structure followed geographic structure; collections from creeks within sub‐drainages were the most closely related, and collections from different tributaries were genetically distinct. Comparisons with cutthroat trout O. clarkii indicated little to no introgression. Comparisons with steelhead (anadromous rainbow trout), coastal rainbow trout O. mykiss irideus, and inland rainbow trout from hatcheries suggested introgression by hatchery fish into some wild populations. Introgression was suspected in populations from stocked tributaries and tributaries that lacked barriers to escaped hatchery fish. Populations from tributaries above barriers that had not been stocked were genetically distinct from hatchery fish and appeared to be native inland redband trout O. mykiss gairdneri.

An analysis of the population genetics of potential multi-drug resistance inWuchereria bancroftidue to combination chemotherapy

Currently, annual mass treatments with albendazole (ABZ) plus ivermectin (IVM) or diethylcarbamazine (DEC) are administered under the Global Programme to Eliminate Lymphatic Filariasis (GPELF). Drug resistance against both ABZ and IVM is prevalent in nematodes of veterinary importance, raising awareness that if anthelmintic resistance were to develop among Wuchereria bancrofti populations, this would jeopardize GPELF's goals. Genetic structure was incorporated into an existing transmission dynamics model for lymphatic filariasis (LF) to investigate the potential development of concurrent resistance to ABZ and IVM. The resultant models explore the impact of different inheritance modes of resistance to ABZ and IVM on the likely risk of treatment failure under our model assumptions. Results indicate that under ABZ+IVM combination, selection for resistance to one drug is enhanced if resistance to the other drug is already present. Excess parasite homozygosity may increase selection for dominant IVM resistance via enhancing the frequency of recessive ABZ resistance. The model predicts that if multiple resistance genes are associated with different efficacy properties of a drug combination, then examining changes at single loci may be misleading. Sampling schemes in genetic epidemiological surveys investigating the frequency of an allele under selection should consider host age, as individuals of different ages may acquire parasites at different rates.

The impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations determined by RAPD markers

To determine the possible impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations, three natural and three over-exploited (human degraded) populations of the species in the Mediterranean region of Turkey were investigated with Randomly Amplified Polymorphic DNA (RAPD). With the 80 RAPD primers tested, 12 of them yielded 137 polymorphic RAPD fragments. Four of the studied populations maintained unique fragments. The mean proportion of polymorphic fragments for all populations ranged from 89.8 to 98.9% and there were no significant differences between natural (94.8%) vs. over-exploited populations (92.7%). The estimated heterozygosity values suggested that Turkish red pine maintains high levels of genetic diversity (range 0.24–0.28) though studied populations and grouped ones as natural (H = 0.28) vs. over-exploited (0.27) did not differ significantly. The mean F value indicated that the large portion of the total genetic diversity was within populations (93%), but this value was lower in the natural populations (92%) than in the over-exploited ones (94%). In over-exploited populations, excess of homozygosity was observed (about 6% higher) as compared to natural populations, indicating impacts of inbreeding in P. brutia.eST