A Comparative Analysis of ISSR and RAPD Markers for Study of Genetic Diversity in Shisham (Dalbergia sissoo)

Abstract

Shisham (Dalbergia sissoo) is one of the most preferred timber tree species of South Asia. Two DNAbased molecular marker techniques, intersimple sequence repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in this species. A total of 30 polymorphic primers (15 ISSR and 15 random) were used. Amplification of genomic DNA of 22 genotypes, using ISSR analysis, yielded 117 fragments, of which 64 were polymorphic. Number of amplified fragments with ISSR primers ranged from five to ten and varied in size from 180 to 1,900 bp. Percentage polymorphism ranged from 0 to 87.5. The 15 RAPD primers produced 144 bands across 22 genotypes, of which 84 were polymorphic. The number of amplified bands varied from five to 13, with size range from 180 to 2,400 bp. Percentage polymorphism ranged from 0 to 100, with an average of 58.3 across. RAPD markers were relatively more efficient than the ISSR assay. The mental test between two Jaccard's similarity matrices gave r≥0.90, showing very good fit correlation in between ISSR-and RAPD-based similarities. Clustering of isolates remained more or less the same in RAPD and combined data of RAPD and ISSR. The similarity coefficient ranged from 0.734 to 0.939, 0.563 to 0.946, and 0.648 to 0.920 with ISSR, RAPD, and combined dendrogram, respectively.

Comparison of RAPD and ISSR markers for assessment of genetic diversity among endangered rare Dalbergia oliveri (Fabaceae) genotypes in Vietnam

“…This finding is opposite to that reported by Arif et al (2009), who worked with Shisham (D. sisso). Some researchers have shown that ISSR markers are distributed throughout the genome and may be associated with functionally important loci (Penner, 1996;Esselman et al, 1999), while RAPD markers are located in non-coding regions and therefore are selectively neutral (Bachmann, 1997;Landergott et al, 2001 …”

“…We found high genetic variability among different genotypes of D. oliveri in the Yok Don National Park. RAPD and ISSR molecular markers have been commonly used in population genetics studies and for detecting clonal diversity in many species (Parsons et al, 1997;Esselman et al, 1999;Li and Ge, 2001;Chen et al, 2006;Gupta et al, 2008;Arif et al, 2009 (Rout et al, 2003). Andrianoelina et al (2006) also quantified and analyzed the genetic variation of D. monticola, using RAPDs.…”

“…RAPD (Williams et al, 1990) and ISSR markers (Zietkiewicz et al, 1994) are two widely applicable techniques to identify relationships at the species and cultivar levels (Raina et al, 2001;Martins et al, 2003;Gupta et al, 2008;Arif et al, 2009), because they are rapid, simple to perform and inexpensive; they do not require prior knowledge of DNA sequences and only a small amount of DNA is needed (Esselman et al, 1999). Genetic diversity of some Dalbergia species has been evaluated with molecular techniques; however, genetic studies of rare and valuable Dalbergia species of Vietnam, which are in danger of extinction due to overexploitation, have not been reported.…”

Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

“…In some studies these markers show very close results, for example 85.4% and 85.2% polymorphic fragments, respectively (Liu et al 2008). There are also enough works suggesting that RAPD-PCR exceeds ISSR-PCR by the ability to reveal polymorphism (Venkatachalam et al 2008;Farajpour et al 2011, Lalhruaitluanga & Prasad 2009Arif et al 2009;Gupta et al 2008;Mishra 2009;Xavier et al 2011;Biswas et al 2010). It seems possible that differences in the effectiveness of various marker systems are related to differences in genome structure of species under study, namely to proportion of coding and non-coding sequences within the genome.…”

Application of ISSR markers for verification of F1 hybrids in mungbean (Vigna radiata)

“…ElHady et al (2010) have shown that individual or combined RAPD and ISSR markers can be used effectively to determine genetic relationships among Vigna species. Similarly, both RAPD and ISSR markers have been used in genetic diversity analysis and genotype identification in plants such as banana, betel vine, castor, elephant grass, rice bean, shisham, and tea (Devarumath et al, 2002;Lakshmanan et al, 2007;Muthusamy et al, 2008;Arif et al, 2009;Gajera et al, 2010;de Lima et al, 2011;Patra et al, 2011). Many authors have found that ISSR markers are highly polymorphic and exhibit higher levels of efficiency, reproducibility, and accuracy than those of RAPD markers (Souframanien and Gopalakrishna, 2004;Ghalmi et al, 2010;Ali et al, 2011).…”