Development of Microsatellite Markers for Tanacetum cinerariifolium (Trevis.) Sch. Bip., a Plant with a Large and Highly Repetitive Genome

Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevis.) Sch. Bip.) is an outcrossing plant species (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repeatability and large genome (1C-value = 9.58 pg) our previous attempts to develop microsatellite markers using the traditional method were unsuccessful. Now we have used Illumina paired-end whole genome sequencing and developed a specific procedure to obtain useful microsatellite markers. A total of 796,130,142 high-quality reads (approx. 12.5× coverage) were assembled into 6,909,675 contigs using two approaches (de novo assembly and joining of overlapped pair-end reads). A total of 31,380 contigs contained one or more microsatellite sequences, of which di-(59.7%) and trinucleotide (25.9%) repeats were the most abundant. Contigs containing microsatellites were filtered according to various criteria to achieve better yield of functional markers. After two rounds of testing, 17 microsatellite markers were developed and characterized in one natural population. Twelve loci were selected for preliminary genetic diversity analysis of three natural populations. Neighbor-joining tree, based on the proportion of shared alleles distances, grouped individuals into clusters according to population affiliation. The availability of codominant SSR markers will allow analysis of genetic diversity and structure of natural Dalmatian pyrethrum populations as well as identification of breeding lines and cultivars.

High diversity of natural Dalmatian pyrethrum based on pyrethrin composition at intra- and interpopulation level

Seeds collected from 10 Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip. Asteraceae) populations naturally occurring along the Adriatic coast and islands, were used to establish a common garden with the aim of estimating the variation of pyrethrin compounds between and within populations. A recently optimized matrix solid phase dispersion (MSPD) method was used for the extraction of six pyrethrin compounds from dry flower heads of 200 Dalmatian pyrethrum individuals. Separation and quantification of pyrethrin compounds were performed by high performance liquid chromatography with diode array detector (HPLC-DAD). High variability in pyrethrin content and composition was observed within and between populations. Total pyrethrin content in individual samples varied from 0.10% to 1.35% of flower dry weight. On average, the lowest total pyrethrin content was observed in the population of Pelješac (0.22%) and the highest in the island populations of Mali Lošinj and Zlarin (0.87%). The population of Mali Lošinj had the most favourable pyrethrin profile, including the lowest variability in total pyrethrin content, the highest pyrethrin I (PI) content (up to 60.47%) and PI/PII ratio (up to 5.88), as well as the lowest pyrethrin II (PII) content. In contrast, the populations from Biokovo and Pelješac represented pyrethrin profiles with the lowest content of total pyrethrin, PI and PI/PII ratio. The Biokovo population also had the highest PII content (43.18% on average), while the Pelješac population had the highest jasmolin I (JI) and jasmolin II (JII) content. Four different chemotypes were determined by cluster analysis. Chemotype P1 is the most promising for future breeding programs and is characterized by the highest total pyrethrin content, PI content and PI/PII ratio, as important measures of insecticidal activity. Correlation analysis of each pyrethrin compound with 25 environmental variables and Principal Component Analysis (PCA) were carried out and the importance of optimum temperature and precipitation on pyrethrin quantity and quality was suggested. Total pyrethrin content was significantly correlated with six temperature and five precipitation parameters. Pyrethrin I, PII and cinerin II (CII) were significantly correlated mainly with temperature parameters; JII and cinerin I (CI) with precipitation parameters, while JI was correlated with temperature range and precipitation parameters. The mountainous Biokovo population was an outlier in the PCA analysis, mainly due to the extremely low values of temperature parameters at a higher altitude. Precipitation variables separated the central Adriatic islands inhabiting drier habitats from populations inhabiting habitats with greater precipitation. The high-resolution data from this study provide the opportunity for individual-based selection for breeding plants with the best pyrethrin profiles, as well as for increased adaptation to broader climatic conditions.

Maternal genetic heritage of Southeastern Europe reveals a new Croatian isolate and a novel, local sub-branching in the x2 haplogroup

High mtDNA variation in Southeastern Europe (SEE) is a reflection of the turbulent and complex demographic history of this area, influenced by gene flow from various parts of Eurasia and a long history of intermixing. Our results of 1035 samples (488 from Croatia, 239 from Bosnia and 130 from Herzegovina, reported earlier, and 97 Slovenians and 81 individuals from Žumberak, reported here for the first time) show that the SEE maternal genetic diversity fits within a broader European maternal genetic landscape. The study also shows that the population of Žumberak, located in the continental part of Croatia, developed some unique mtDNA haplotypes and elevated haplogroup frequencies due to distinctive demographic history and can be considered a moderate genetic isolate. We also report seven samples from the Bosnian population and one Herzegovinian sample designated as X2* individuals that could not be assigned to any of its sublineages (X2a'o) according to the existing X2 phylogeny. In an attempt to clarify the phylogeny of our X2 samples, their mitochondrial DNA has been completely sequenced. We suppose that these lineages are signs of local microdifferentiation processes that occurred in the recent demographic past in this area and could possibly be marked as SEE-specific X2 sublineages.

Maternal genetic legacy of the eastern Adriatic island of Krk--an interplay of evolutionary forces and island's historical events in shaping the genetic structure of contemporary island population

This study presents genetic diversity and structure of contemporary Krk islanders revealed by high-resolution mitochondrial DNA analysis on a sample of 132 unrelated autochthonous adults from seven different settlements and regions of the island. Relatively high level of haplogroup and haplotype diversity in the overall island sample is an indicator of numerous migrations and gene flows throughout the history. Expectedly, the results show the highest frequency of haplogroup H (33.3%), yet this value is much lower compared to different Croatian and other European mainland populations. An interesting finding refers to highly elevated frequencies of some haplogroups, otherwise rare in Croatia and most of the Europe, such as I (11.3%) and W (7.6%) in Krk population, especially pronounced in some settlements. At the level of settlements, many of the major European haplogroups were found to be absent from their mtDNA gene pools, whereas several others show a pronounced deviation from an average. Overall, our results suggest a tangled interplay of different evolutionary forces, such as founder effects and a few strong bottlenecks, presumably due to epidemics, which have occurred in various periods of the island's history. Cultural customs, such as frequent endogamy in some regions of the island during past centuries, have additionally shaped its genetic structure into the observed present-day diversity patterns.

Influence of evolutionary forces and demographic processes on the genetic structure of three Croatian populations: a maternal perspective

BACKGROUND

Many Croatian islands are examples of genetic isolates, with low level of heterozygosity and high level of inbreeding, due to practice of endogamy.

AIM

The aim was to study the genetic structure of two insular and one mainland population through high-resolution phylogenetic analysis of mitochondrial DNA (mtDNA).

SUBJECTS AND METHODS

MtDNA polymorphisms were explored in 300 unrelated individuals from Mljet, Lastovo and the coastal city of Dubrovnik, based on SNP polymorphisms.

RESULTS

All mtDNA haplogroups found in the sample were of typical European origin. However, the frequency distribution of their subclades differed significantly from other Croatian and European populations. MtDNA haplotype analysis revealed only two possible founder lineages on Mljet and six on Lastovo, accounting for almost half of the sample on both islands. The island of Mljet also has the lowest reported haplotype and nucleotide diversity among Croatian isolates and the island of Lastovo, a new sublineage of a usually quite rare U1b clade.

CONCLUSION

The results can be explained by the effect evolutionary forces have on genetic structure, which is in line with the specific demographic histories of the islands. An additional research value of these two island isolates is the appearance of certain Mendelian disorders, highlighting their importance in epidemiological studies.

Replication of genetic variants from genome-wide association studies with metabolic traits in an island population of the Adriatic coast of Croatia

Twenty-two single-nucleotide polymorphisms (SNPs) in 10 gene regions previously identified in obesity and type 2 diabetes (T2D) genome-wide association studies (GWAS) were evaluated for association with metabolic traits in a sample from an island population of European descent. We performed a population-based study using 18 anthropometric and biochemical traits considered as continuous variables in a sample of 843 unrelated subjects (360 men and 483 women) aged 18-80 years old from the island of Hvar on the eastern Adriatic coast of Croatia. All eight GWAS SNPs in FTO were significantly associated with weight, body mass index, waist circumference and hip circumference; 20 of the 32 nominal P-values remained significant after permutation testing for multiple corrections. The strongest associations were found between the two TCF7L2 GWAS SNPs with fasting plasma glucose and HbA1c levels, all four P-values remained significant after permutation tests. Nominally significant associations were found between several SNPs and other metabolic traits; however, the significance did not hold after permutation tests. Although the sample size was modest, our study strongly replicated the association of FTO variants with obesity-related measures and TCF7L2 variants with T2D-related traits. The estimated effect sizes of these variants were larger or comparable to published studies. This is likely attributable to the homogenous genetic background of the relatively isolated study population.

Mitochondrial DNA heritage of Cres Islanders--example of Croatian genetic outliers

Diversity of mitochondrial DNA (mtDNA) lineages of the Island of Cres was determined by high-resolution phylogenetic analysis on a sample of 119 adult unrelated individuals from eight settlements. The composition of mtDNA pool of this Island population is in contrast with other Croatian and European populations. The analysis revealed the highest frequency of haplogroup U (29.4%) with the predominance of one single lineage of subhaplogroup U2e (20.2%). Haplogroup H is the second most prevalent one with only 27.7%. Other very interesting features of contemporary Island population are extremely low frequency of haplogroup J (only 0.84%), and much higher frequency of haplogroup W (12.6%) comparing to other Croatian and European populations. Especially interesting finding is a strikingly higher frequency of haplogroup N1a (9.24%) presented with African/south Asian branch almost absent in Europeans, while its European sister-branch, proved to be highly prevalent among Neolithic farmers, is present in contemporary Europeans with only 0.2%. Haplotype analysis revealed that only five mtDNA lineages account for almost 50% of maternal genetic heritage of this island and they present supposed founder lineages. All presented findings confirm that genetic drift, especially founder effect, has played significant role in shaping genetic composition of the isolated population of the Island of Cres. Due to presented data contemporary population of Cres Island can be considered as genetic "outlier" among Croatian populations.

Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a

Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.

Association of tagging single nucleotide polymorphisms on 8 candidate genes in dopaminergic pathway with schizophrenia in Croatian population

AIM

To perform a comprehensive evaluation of association of common genetic variants in candidate genes in the dopaminergic pathway with schizophrenia in a sample from Croatian population.

METHODS

A case-control association study was performed on 104 unrelated patients with schizophrenia recruited from a psychiatric hospital in Zagreb and 131 phenotypically normal Croatian subjects. Forty-nine tagging single nucleotide polymorphisms (tagSNPs) in 8 candidate genes in the dopaminergic pathway were identified from the HapMap database and tested for association. Genotyping was performed using the SNPlex platform. Statistical analysis was conducted to assess allelic and genotypic associations between cases and controls using a goodness of fit chi(2) test and trend test, respectively; adjustment for multiple testing was done by permutation based analysis.

RESULTS

Significant allele frequency differences between schizophrenia cases and controls were observed at 4 tagSNPs located in the genes DRD5, HTR1B1, DBH, and TH1 (P<0.005). A trend test also confirmed the genotypic association (P<0.001) of these 4 tagSNPs. Additionally, moderate association (P<0.05) was observed with 8 tagSNPs on SLC6A3, DBH, DRD4, SLC6A4, and COMT.

CONCLUSIONS

Common genetic variants in genes involved in the dopaminergic pathway are associated with schizophrenia in the populations of Caucasian descent.

Population genetics of 15 AmpflSTR Identifiler loci in Macedonians and Macedonian Romani (Gypsy)

Allele frequencies of 15 AmpFlSTR Identifiler STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were analysed in a sample of 100 unrelated autochthonous Macedonian and 102 Macedonian Romani individuals, representing different ethnic groups residing within the same country of Former Yugoslav Republic of Macedonia. The interpopulation comparisons between Macedonians and Macedonian Romani with four south eastern European populations, Kosovo Albanians, Serbians from Vojvodina Province, western Romanians and northern Greeks were performed as well as comparison between Macedonian Romani and Assam population from Asia (India). Reported data point that Macedonian Romani, as an example of an endogamous population of Asian (Indian) origin, show significant allelic differences when compared to neighbouring south eastern European populations.

Genetic diversity of 15 STR loci in a population of Montenegro

Genetic diversity and forensic parameters based on 15AmpFlSTR Identifiler short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were evaluated in a sample of 101 unrelated, autochthonous adults from Montenegro. After applying Bonferroni correction, the agreement with Hardy-Weinberg equilibrium (HWE) was confirmed for all loci with the exception of D5S818 (chi2 test) and D21S11 (exact test). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.9999999999999999844 and 0.99999382, respectively. According to measures of within-population genetic diversity, D2S1338, D18S51 and FGA may be considered as the most variable and most informative markers for forensic testing and population genetic analyses out of the 15 analysed loci in a population of Montenegro. D5S818 showed to be the least variable and together with TPOX, the least informative. Interpopulation comparisons were carried out and levels of genetic differentiation between population of Montenegro and five South-eastern European populations (Kosovo Albanians, Serbians from Vojvodina province, Macedonians, Bosnians and Croatians) were evaluated. The most differentiated population in relation to Montenegro is a population of Kosovo Albanians as suggested by both AMOVA and coefficients of genetic differentiation (F(ST) and R(ST)).