ASSESSMENT OF GENETIC DIVERSITY IN SOME WILD PLANTS OF ASTERACEAE FAMILY BY RIBOSOMAL DNA SEQUENCE

M Amar,A Hassan,Esraa El Sherbeny

doi:10.21608/ejgc.2012.10534

M Amar, A Hassan + Show 1 more

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https://doi.org/10.21608/ejgc.2012.10534

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Abstract

Ribosomal DNA genes are organized in clusters of tandem repeated units, each of which consists of coding regions (18S, 5.8S and 28S) and two internal transcribed spacers (ITS), in addition to intergenic spacer (IGS) region. Accordingly this article is focused on clarifying the sequence divergence of complete rDNA of ITS and IGS regions among four wild and endemic species of Asteraceae family in Egypt. Results indicated that there were a total of 754 and 667 positions across the final dataset for ITS and IGS sequences, respectively. IGS regions were superior compared to ITS region in several parameters like nucleotide diversity rate (π = 0.60), the estimated values of transition/transversion rate ratios (k1 = 38.28, purines), (K2 = 12.58, pyrimidines) and the overall transition/transversion bias (R = 12.10), respectively. This reflects that transitions are more dominant than transversion in Asteraceae germplasm across IGS markers. Thus, it was concluded that the IGS region could be more suitable for measuring genetic relationship in different subspecies of Asteraceae, with more informative sites than ITS sequences. Generally ribosomal DNA particularly intergenic spacer of the rDNA cluster evolves quickly and is highly polymorphic, providing a useful tool for assessing genetic diversity, taxonomic and phylogenetic studies in Asteraceae germplasm.

Highlights

With the rapid development of molecular biology studies of Asteraceae germplasm identification and genetic diversity offer numerous reliable molecular marker information by means of Random Amplified Polymorphic DNA (RAPD) (Badr et al, 2012), Restriction Fragment Length Polymorphism (RFLP) (Ito et al, 2000), Inter-simple sequence repeat (ISSR) (Gharibi et al, 2011), Simple Sequence Repeat (SSR) (Simko, 2009), RAPD, ISSR and RFLP (Abd El-Tawab et al, 2010), amplified fragment length polymorphisms (AFLP) (Czarnecki et al, 2008) etc
We examined the molecular divergence of complete rDNA sequenced of internal transcribed spacers (ITS) and intergenic spacers (IGS) regions among four wild species of Asteraceae germplasm in Egypt
Variation was observed in the nucleotide composition of the ITS and IGS, which may be due to the sequence length variation of the analyzed markers (Table 2)

Summary

Introduction

With the rapid development of molecular biology studies of Asteraceae germplasm identification and genetic diversity offer numerous reliable molecular marker information by means of Random Amplified Polymorphic DNA (RAPD) (Badr et al, 2012), Restriction Fragment Length Polymorphism (RFLP) (Ito et al, 2000), Inter-simple sequence repeat (ISSR) (Gharibi et al, 2011), Simple Sequence Repeat (SSR) (Simko, 2009), RAPD, ISSR and RFLP (Abd El-Tawab et al, 2010), amplified fragment length polymorphisms (AFLP) (Czarnecki et al, 2008) etc. A nontranscribed spacer (NTS) separates adjacent copies of the rDNA repeat unit Both spacers (ETS and NTS) are called intergenic spacers (IGS) (Dabert et al, 2006).The major concerns with the use of the rDNA locus in taxonomic and phylogenetic analyses are the existence of polymorphisms among repeated units, which may cause extensive differentiation even within a single individual and provide useful tools for phylogenic studies (Wei et al, 2010). Sequence comparison of the rDNA region is widely used in taxonomy and molecular phylogeny It has typically been most constructive for variation between species, populations and even individuals (or inbred lines) as in tomato (Jo et al, 2009), rice (Chang et al, 2010), apple (Giaretta et al, 2010), and Compositae, Anthemideae (Sonboli et al, 2012). Even there has been no report about the comparison of ITS and IGS sequences and their efficiency and utility as molecular markers in Asteraceae family

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