Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment

Abstract

ABSTRACT. Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into 10589 Utility of iPBS retrotransposons in okra ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 10588-10602 (2015) four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra.

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

“…We found that band profiles remain unchanged after repeating the PCR amplification for both primers. Total and polymorphic numbers of bands remained unchanged ( Figure S2) and these results were found similar to the previous studies [41,53]. These results are confirming the higher reproducibility of this marker system.…”

“…They found similar clustering for species and confirmed the trustbility and robustness of this marker system. Yildiz et al [53] also checked the reproducibility of this marker system in okra by repeating PCR two times and stated that band profiles remains unchanged after PCR amplification. In this study, we also checked the reproducibility of the iPBS-retrotransposon marker system by repeating PCR two times for two primers.…”

Population structure and linkage disequilibrium in a large collection of Fusarium oxysporum strains analysed through iPBS markers

“…The average Nei's genetic diversity ( h ) and Shannon's information index ( I ) among our 160 isolates belonging to four different pathogenic strains of F. oxysporum were found to be 0.23 and 0.47, respectively (Table ), which were in agreement with the findings obtained by Ben‐Jin et al () and Ozer et al (), showing a low level of differentiation. On the other hand, Yildiz, Kocak, and Baloch () reported that the genetic diversity ( h ) and Shannon's information index ( I ) of iPBS‐retrotransposon markers were lower than those of SSR markers, indicating that iPBS‐retrotransposon markers are more efficacious in determining genetic diversity.…”

GENETIC DIVERSITY OF CROCUS SATIVUS AND ITS CLOSE RELATIVE SPECIES ANALYZED BY iPBS-RETROTRANSPOSONS

“…In current study, the average Nei's genetic diversity (h) and Shannon's information index (I) among saffron genotypes and its close relative species were 0.16 and 0.29, respectively (Table 3), indicating a low level of differentiation. Similarly, the mean Shannon's information index for iPBS-retrotransposon markers was reported to be 0.12 (Yildiz et al, 2015) and 0.27 by (Mehmood et al, 2013).…”