Volume 1, Issue 1 , Pages 262-263, August 2008
Polymorphism of mitochondrial DNA D-loop in Rimini and Valmarecchia areas in the North of Italy
Article Outline
- Abstract
- 1. Introduction
- 2. Materials and methods
- 3. Results and discussion
- Conflict of interest
- References
- Copyright
Abstract
The sequence polymorphisms of the hypervariable segments I and II (HVI and HVII) of the human mitochondrial DNA (mtDNA) in two population samples from Romagna region in the North of Italy, the urban area of Rimini and the near area of Valmarecchia, were analyzed. The aim of this study was to create a population database for mtDNA HVI and HVII regions of these two areas. A total of 83 and 80 samples of unrelated individuals from Rimini and Valmarecchia respectively were collected. A phylogenetic analysis was performed following EMPOP program. The principal European haplogroups were found, being the haplogroup H the most frequent. Point heteroplasmy was observed in only two individuals, but the majority of samples showed length heteroplasmy in HVII region. For forensic purpose the observed data may be included in the general Italian database.
Keywords: Mitochondrial DNA, Population data, North of Italy, HVI and HVII
1. Introduction
The characteristics of mitochondrial DNA (mtDNA) are exploited for studying human polymorphism and population substructure, inferring informations about human migration events and creating a forensic database useful in casework. It was seen that mtDNA databases are generally suboptimal for forensic purposes and it was recalled that there is no precedent for a useful a posteriori check on the quality of sequence data as is provided by the now rather well characterized mtDNA phylogeny, which has the potential to prevent most errors and to allow the evaluation of the accuracy of mtDNA databases [1]. The sequence polymorphisms of the hypervariable segments I and II (HVI and HVII) of the human mtDNA in two population samples from Romagna region in the North of Italy, the urban area of Rimini and the near area of Valmarecchia, were analyzed. The aim of this study was to create a population database for mtDNA HVI and HVII regions of these two areas with different geographically and historically backgrounds, being Rimini an important port on Adriatic sea during Roman age and Valmarecchia an isolated area near Rimini.
2. Materials and methods
We analyzed DNA samples from 163 unrelated and healthy individuals, 83 from Rimini and 80 from Valmarecchia area according to each subject's birthplace. Amplification primers were F15997/R16401 (HVS-I) and F29/R408 (HVS-II). Sequencing was performed using BigDye Terminator Cycle Sequencing Ready Reaction Kit v1.1 and sequence products were analyzed using ABI Prism 310 capillary electrophoresis (Applied Biosystems). Sequences were compared with the revised Cambridge Reference Sequence (rRCS). The sequences were scrutinized twice by two independent scientists and then evaluated for potential artificial recombination [2] and a posteriori by phylogenetic analysis following EMPOP program [3]. Molecular diversity indices, analysis of molecular variance (AMOVA) and pairwise differences were estimated with the ARLEQUIN software (Version 3.01). Genetic differentiation between the two populations was evaluated by conventional F-statistics based on haplotypes frequencies. Samples were divided into haplogroups according to patterns of diagnostic polymorphisms.
3. Results and discussion
Complete HVS-I and HVS-II sequences of 163 unrelated individuals were obtained, 76 and 69 mtDNA haplotypes for Rimini and Valmarecchia samples were observed respectively. Considering length variants in the C-stretch regions, 111 for Rimini and 117 for Valmarecchia polymorphic sites were detected. The most frequent haplotype (16224C, 16311C, 73G, 263G, 315.1C), that belong to haplogroup K, was shared in six individuals (3.7%). In only two samples of Rimini population study we observed point heteroplasmy: K_16093Y and H*_16170R; we considered positions as heteroplasmic when the height of the secondary peak was at least 30% of the main peak. The principal European haplogroups were found, being the haplogroup H the most frequent. Fig. 1 shows the distribution of haplogroups in Rimini and Valmarecchia samples. The diversity and genetic parameters are reported in Table 1. The analysis of molecular variance (AMOVA) in the HVI and HVII regions shows that 99.6% of the variation present in the total sample is attributable to within-population diversity, while there are essentially no differences between the two populations (data not shown). A posteriori data analysis regardless of the sequence quality was performed by the software package Network available via the EMPOP website, the t′-value describing a star-like of the network.
Fig. 1.
mtDNA haplogroups distribution in the populations of Rimini and Valmarecchia.
Table 1. Diversity and genetic parameters in the two populations
| Rimini | Valmarecchia | |
|---|---|---|
| Sample size | 83 | 80 |
| No. of haplotypes | 76 | 69 |
| No. of polymorphic positions | 111 | 117 |
| Nucleotide diversity | 0.010786 ±0.005552 | 0.011281±0.005792 |
| Mean number of pairwise differences | 9.168087±4.259279 | 9.589241±4.442850 |
Conflict of interest
None.
References
PII: S1875-1768(08)00068-1
doi:10.1016/j.fsigss.2007.10.033
© 2008 Elsevier Ireland Ltd. All rights reserved.
Volume 1, Issue 1 , Pages 262-263, August 2008
