Genetic structure and diversity of Adonis L. (Ranunculaceae) populations collected from Turkey by inter-primer binding site (iPBS) retrotransposon markers

Abstract

The genus Adonis L. is a member of Ranunculaceae and consists of perennial and annual herbaceous plants included in the tribe Adonideae under the subfamily Ranunculoideae. Botanically, Ranunculaceae comprises vital medicinal plants. Molecular markers are one of the most effective tools for exploring genetic variation that can enhance breeding efficiency. To identify the genetic diversity of 62 Adonis ecotypes collected from different regions in Turkey, the interprimer binding site (iPBS) retrotransposon system was used. Of the 83 iPBS primers used, 10 provided sufficient polymorphic data, generating a total of 204 alleles. The number of iPBS bands per individual was 3.29, and the number of alleles per polymorphic locus ranged from 8 to 35, with an average of 20.30. The average polymorphism percentage was 99.50%, and polymorphic information content ranged from 0.16 to 0.39. The highest average number of alleles, Nei's genetic diversity (h), and Shannon's information index (I) were obtained from A. volgensis species (1.64, 0.39, and 0.58, respectively), whereas the lowest values (1.41, 0.29, and 0.46, respectively) were found in A. flammea species. The analysis of molecular variance revealed significant variance within the population (71%), whereas no significant genetic variation was observed among the different species (29%). Cluster analysis according to unweighted pair-group mean average (UPGMA) divided 62 Adonis ecotypes into four major clusters. According to the principal coordinate analysis, the first three principal coordinates accounted for 81.51% of total variation. Genetic structure analysis of the studied germplasm using the Bayesian method revealed four subpopulations with an average of 0.2634 for expected heterozygosity and 0.2154 for population differentiation measurements. The results of this study suggested that iPBS markers could be used in the identification of genetic diversity among the Adonis species.

Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

“…In this study, the mean PIC value was 0.361 which varied 0.163-0.585. Mean PIC value obtained in this study was found much greater than reported by earlier studies using iPBS-retrotransposons markers [25,49].…”

“…Analysis of molecular variance (AMOVA) revealed the existence of higher variations within the laurel genotypes and the percentage of the total variance was 85% (Table 4). Pour et al [49] stated that higher variations within genotypes might be due to selection, adaptation, gene flow, genetic drift, variation in ecotypes and the pollination method. Moreover, human activities and environmental fluctuations over time might be responsible for higher variations [55].…”

SSR-Based Molecular Identification and Population Structure Analysis for Forage Pea (Pisum sativum var. arvense L.) Landraces

“…PCR Amplification was performed in a thermos cycler (SensoQuest Labcycler, Göttingen, Germany) and was conducted in 10 µL reaction mixture comprising 25 ng template DNA, 0.5 U Taq polymerase, 0.25 mM dNTP, 1 µM (20 pmol) primer, 10X buffer; 2 mM MgCl 2 . The PCR thermal cycling profile was as follows: initial denaturation for 3 min at 95 °C, 38 cycles of 95 °C for 60 s, 53–66 °C (annealing temperature depending on primers; for details see Table 2 ) for 60 s, 72 °C for 120 s, and final extension at 72 °C for 10 min [ 22 ]. At 200 V for 105 min, all PCR amplification products were separated by polyacrylamide Mega-Gel dual vertical electrophoresis (Model C-DASG-400-50).…”

iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye

“…PCR Amplification was performed in a thermos cycler (SensoQuest Labcycler) and were conducted in 10 µL reaction mixture comprising 25 ng template DNA, 0.5 U Taq polymerase, 0.25 mM dNTP, 1 µM (20 pmol) primer, 1X buffer; 2 mM MgCl2. The PCR thermal cycling profile is as follow; initial denaturation for 3 min at 95 • C, 38 cycles of 95 • C for 60 s, 50-60 • C for 60 s, 72 • C for 120 s and final extension at 72 • C for 10 min [29]. All PCR amplification products were resolved in agarose gel at 3% concentration at 200 V for 105 min.…”