ITS, RAPD-PCR and ISSR-PCR are most popular DNA-based techniques that are extensively applied in the determination of the genetic diversity of species among populations. However, especially for organisms having high genetic polymorphism, phylogenetic trees drawn from the results of these techniques may be different. For finding a meaningful phylogenetic tree, it should be compared phylogenetic trees obtained from these different techniques with geographic locations of populations. Lichens have a high genetic polymorphism and tolerance against different environmental conditions. In this study, these three DNA-based genetic diversity techniques were compared, using different populations of a lichen species (Xanthoria parietina). X. parietina was especially chosen because of its high genetic diversity in narrow zones. Lichen samples were collected from ten different locations in a narrow transition climate zone Bilecik (Turkey). Statistical analyses of all results were calculated using UPGMA analysis. Phylogenic trees for each technique were drawn and transferred to the Bilecik map for comparative analysis. The results of three techniques allowed us to verify that populations of X. parietina have high genetic variety in a narrow zone. But phylogenetic trees obtained from these results were found to be very different. Our comparative analysis demonstrated that the results of these techniques are not similar and have critical differences. We observed that the ITS method provides more clear data and is more successful in genetic diversity analyses of more asunder populations, in contrast to ISSR-PCR and RAPD-PCR methods.
Common bunt caused by Tilletia sp. is a very destructive and dangerous seed-borne fungal disease and may cause serious economic losses in worldwide. Wheat cultivars carrying resistance genes are used as an alternative fight method instead of chemical fungicides against common bunt disease. These resistance genes in wheat are called as bt genes. Until today, a few number of bt genes has been detected in wheat by using various molecular markers. However, development of more molecular markers for detection of all bt genes in wheat is required. In this study, detection of five bt genes called as bt -5, bt-8, bt-10, bt-11 and bt-12 was carried in ten registered local wheat varieties (Sertak 52, Bolal 2973, Demir, Kutluk, Harmankaya 99, Pehlivan, Tosun Bey, 4-11, Sönmez 01, Bezostaja-1) using PCR-based molecular markers, microsatellite and RAPD. PCR-amplified fragments were separated on 1.3% agarose gel. The obtained DNA bands were scored as present or absent for detection of bt genes. For comparison, the virulence rates of five Tilletia foetida (syn. leaves) isolates against ten wheat varieties were obtained from our field results. We observed that wheat varieties Kutluk and 4-11 carrying bt-10 and bt11 genes are more resistant to disease in field. -5, bt-8, bt-10, bt-11 and bt-12) tespiti gerçekleştirilmiştir. PCR ile çoğaltılan fragmentler, ethidium bromide (0.5 μg/ml) içeren %1.3'lük agaroz jelde ayrılmıştır. Jeller UV ışık altında gözlenmiş ve dijital olarak fotoğraflanmıştır. Elde edilen DNA bantları bt genleri için var veya yok olarak değerlendirilmiştir. Karşılaştırma yapmak için, 10 buğday çeşidine karşı beş Tilletia foetida (syn. leaves) izolatının hastalık yapma oranı tarla verilerinden elde edilmiştir. Kutluk ve 4-11 gibi bt10 ve bt11 genlerini içeren buğday çeşitlerin tarlada hastalığa karşı daha dirençli oldukları gözlenmiştir. Tüm buğday çeşitlerindeki beş bt geni için analiz sonuçları ve tarladaki direnç oranlarını gösterilmiştir.
We successfully used the guanidine isothiocyanate method for isolation of total RNA from leaf, stem, and root tissues of the aromatic plant Origanum onites. The RNA was extracted with TRI Reagent® at room temperature and was recovered by isopropanol precipitation. The isolated RNA was capable of reverse transcription. The extraction method described here does not require ultracentrifugation, and it is fast, simple, and effective. The procedure can be completed within 3 hours and may be applicable to other aromatic medicinal plants containing high amounts of phenolic compounds.
A study of the genetic relationships among Petrorhagia taxa from Turkey was carried out using inter-simple sequence repeat (ISSR) markers. A total of 409 amplified bands were obtained by 10 ISSR primers. The polymorphism ratio was high (100%) across 45 individuals representing nine Petrorhagia taxa (P. dubia, P. prolifera, P. pamphylica, P. peroninii, P. saxifraga, P. cretica, P. alpina subsp. alpina, P. alpina subsp. olympica, P. lycica) and was sufficient to distinguish each species. Statistical analyses were performed by using POPGENE, GenAlEx6, and PAUP. An unweighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on Nei’s genetic distance along with outgroup species (Velezia rigida) in MEGA4. The dendrogram shows two main clusters, the first one (Cluster-I) included only P. lycica, while the cluster-II contained all other taxa. Cluster-II can be grouped in two sub-clusters, with P. prolifera and P. saxifraga constituting a first sub-cluster, the other species (P. alpina subsp. alpina, P. alpina subsp. olympica, P. cretica, P. dubia, P. peroninii and P. pamphylica) being grouped in a second sub-cluster. Both PCoA and Neighbour-Net network analysis supported the dendrogram. The study showed that ISSR technique can be successfully used in species identification and determination of the genetic relationships between Petrorhagia species distributed in Turkey.
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