Elucidating genetic relationships, diversity and population structure among the Turkish female figs

Yazan: admin Tarih: Oca 21st, 2010 | Kategori:: Gene polymorphisms

Ikten H (Ikten, Hatice)2, Mutlu N (Mutlu, Nedim)3, Gulsen O (Gulsen, Osman)1, Kocatas H (Kocatas, Hilmi)4, Aksoy U (Aksoy, Uygun)5

Source: GENETICA Volume: 138 Issue: 2 Pages: 169-177 Published: FEB 2010

Abstract: A collection of 96 female Turkish fig (Ficus carica L.) accessions was studied to elucidate genetic structure and estimate diversity and genetic similarity distribution among the female figs present in Turkish genetic resources, using 157 molecular genome markers including 129 sequence-related amplified polymorphisms, 21 random amplified polymorphic DNAs, and 7 simple-sequence repeats. The plant samples mainly included Turkish fig collections selected throughout the country over the course of a half-century. Neighbor-joining analysis revealed continuous dissimilarity range, and it was difficult to classify figs into distinct groups. The principle component analysis produced similar results. The analysis of molecular variance indicated that 95 and 93% of genetic variation were explained by within geographic origins and similar fruit rind color, respectively. Sub-structuring Bayesian analysis assigned the 96 female figs into four sub-populations, and indicated that they were highly related. The corrected allelic pairwise distances among the six geographic origins were less than 5%. This study suggests that geography- and color-based groups were not genetically distinct among the Turkish figs.
Document Type: Article
Language: English
Author Keywords: Ficus carica; SRAP; Neighbor-joining; PCA; AMOVA; Population structure
KeyWords Plus: FICUS-CARICA L.; GERMPLASM COLLECTION; COMMON FIG; MARKERS; RAPD; RELATEDNESS; GENOTYPES; RFLP; AFLP
Reprint Address: Gulsen, O (reprint author), Erciyes Univ, Dept Hort, Fac Agr, TR-38039 Kayseri, Turkey
Addresses:
1. Erciyes Univ, Dept Hort, Fac Agr, TR-38039 Kayseri, Turkey
2. Minist Agr & Rural Affairs, W Mediterranean Res Inst, TR-07100 Antalya, Turkey
3. Univ Nebraska, George W Beadle Ctr, Dept Biochem, Lincoln, NE 68503 USA
4. Fig Res Inst, TR-09600 Erbeyli, Aydin Turkey
5. Aegean Univ, Fac Agr, Dept Hort, TR-35100 Izmir, Turkey
E-mail Addresses: o_gulsen@yahoo.com


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Genetic Variations in the Hypoxia-inducible Factor-1{alpha} Gene and Lung Cancer.

Yazan: admin Tarih: Ağu 24th, 2009 | Kategori:: Cancer (Kanser), Gene polymorphisms, Lung cancer (Akciğer Kanseri), polymorphisms

Exp Biol Med (Maywood). 2009 Jun 22.

Konac E, Dogan I, Onen IH, Yurdakul AS, Ozturk C, Varol A, Ekmekci A.

Gazi University, Faculty of Medicine.

Hypoxia-inducible factor-1 (HIF-1), an important genetic component of angiogenesis, becomes stable as a response to tumor hypoxia and facilitates tumor survival. The polymorphisms of the HIF-1alpha gene may cause changes in the activity of the protein which serves as a transcription factor for many genes in tumorigenesis. In this study, we have investigated the relationship between seven HIF-1alpha polymorphisms [C>T substitution in intron 8 (rs10873142), T418I (rs41508050) in exon 10, P564P (rs41492849), L580L (rs34005929), P582S (rs11549465), A588T (rs11549467) in exon 12 and dinucleotide GT repeat in intron 13 (rs10645014)] among lung cancer patients in the Turkish population. Genomic DNA was isolated from 141 lung cancer cases and 156 controls and subjected to PCR for amplification. Genotyping was carried out with RFLP and DNA sequencing methods. There was no significant difference between lung cancer cases and controls in terms of the distribution of genotyping frequencies of seven HIF-1alpha polymorphisms (P>0.05). No significant relationship was found between the C>T substitution in intron 8 and P582S haplotypes and development of lung cancer. Also, no significant difference was observed between the genotypes and clinopathological characteristics of the cases. These findings showed that polymorphisms of the HIF-1alpha gene did not confer susceptibility to lung cancer.


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Association of paraoxonase 55 and 192 gene polymorphisms on serum homocysteine concentrations in preeclampsia.

Yazan: admin Tarih: Tem 12th, 2009 | Kategori:: Paraoxonase

Folia Biol (Praha). 2009;55(2):35-40

Isbilen E, Yilmaz H, Arzu Ergen H, Unlucerci Y, Isbir T, Gurdol F.

Department of Biochemistry, Faculty of Medicine, Baskent University, Ankara, Turkey.

Paraoxonase 1 (PON1) is thought to influence serum homocysteine concentrations, at least in part, due to its homocysteine thiolactonase activity and to play a role in preeclampsia and atherosclerosis. We investigated the effects of PON 55 and PON 192 polymorphisms on plasma total homocysteine (tHcy) concentrations in preeclamptic and healthy pregnants among Turkish population (N = 106). PON 55 and 192 genotypes were determined by PCR RFLP techniques. Plasma tHcy concentrations were measured by high-performance liquid chromatography. No differences were observed in the distribution of PON 1 55/192 genotypes and allele frequencies between the preeclamptic and healthy pregnants. tHcy level in the plasma of preeclamptic women was found to be increased in comparison with healthy pregnants (P < 0.01). Preeclamptic women bearing the mutated PON 192 RR and wild-type PON1 55 LL genotypes had higher tHcy levels than those of the healthy pregnants with the corresponding genotypes, supporting the possibility that the hyperhomocysteinaemia seen in preeclamptic women is associated with the PON genotypes. However, no influence of the allelic distribution on plasma tHcy concentrations was detected in either group. Our results suggest that PON1 55 and 192 genotypes might have an important role in developing hyperhomocysteinaemia and may also have a role in the pathogenesis of preeclampsia in a Turkish population.


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Genotype and allele frequencies of MDR1 gene C1236T polymorphism in a Turkish population.

Yazan: admin Tarih: Ara 10th, 2008 | Kategori:: Kategorilenmemiş

Genet Mol Res. 2008 Oct 28;7(4):1193-9.

Gümüŝ-Akay G, Rüstemoğlu A, Karadağ A, Sunguroğlu A.

Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey guvemg@yahoo.com.

Human P-glycoprotein (P-gp) is encoded by the MDR1 gene, which is located on chromosomal region 7q21 and consists of 28 exons. To date, over 50 single nucleotide polymorphisms (SNPs) have been reported for the MDR1 gene. The effect of these polymorphisms on P-gp function or their clinical impact is in most cases unknown, but some of the SNPs are known to be of functional relevance and can also alter the pharmacokinetics of substrate drugs. The aim of the current study was to analyze for the first time an existing silent MDR1 C1236T (Gly412Gly) polymorphism in a Turkish population. The genotype frequencies of C1236T SNP in a Turkish population were also compared with those in other populations. One hundred unrelated healthy subjects (48 females, 52 males) were included in this study and all them were of Turkish ethnicity. The genotyping of the C1236T SNP was performed by the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. The frequencies of the wild-type C and mutant T alleles were 45.5 and 54.5%, respectively. The distribution of C1236T genotype frequencies in our study group was found to be similar to that in Czech, Polish, Portuguese, Russian, Malay, and Japanese populations and different from that in French, German, Chinese, and Indian populations. The distributions of CC, CT, and TT genotypes were 20.0, 51.0, and 29.0%, respectively. Our study provides a framework for future studies concerning the role of polymorphic variants of MDR1 gene in the genesis of various diseases or in designing future pharmacogenetic and pharmacokinetic studies conducted with P-gp substrates in the Turkish population.


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