Elucidating Genetic Diversity among Sour Orange Rootstocks: a Comparative Study of the Efficiency of RAPD and SSR Markers

Abstract

In order to compare the effectiveness of two molecular marker systems, a set of six RAPD and nine SSR markers were used to study the genetic diversity in a population of 46 sour orange accessions, a common rootstock used in almost all citrus orchards in Tunisia. Genetic diversity parameters [average and effective number of alleles, percentage of polymorphism, polymorphic information content (PIC), effective marker index (EMI), and marker index (MI) parameters] for RAPD, SSR, and RAPD + SSR were determined in order to assess the efficiency of the two marker systems. The results revealed that these parameters were significantly higher when using RAPD markers. Similarly, cluster analysis using the results of RAPD was practically the same as that obtained when combining data from the two marker systems (RAPD + SSR) demonstrating the efficiency of RAPD in discriminating between sour orange accessions. Therefore, the use of SSR markers, known to be more efficient and discriminatory, does not bring significant supplementary information in this work. Indeed, results would have been obtained using only the RAPD markers. Accordingly, this work highlights the efficiency and advantages of RAPD, as an easy and efficient technique, in studying citrus rootstock's genetic diversity, and establishing genetic relationships among citrus accessions.

Characterization of Key Aroma Compounds and Construction of Flavor Base Module of Chinese Sweet Oranges

“…Up until now, approximately 80 aroma compounds have been determined in orange juices, of which 15 volatile components presented odor activity values (OAVs) greater than 1, with dl-limonene, nootkatone and linalool being those with the highest OAVs in both cultivars [9,10]. To better understand the diversity and interrelationship of different sweet orange cultivars, morphological and RAPD markers have been applied in classification [11,12,13,14]. Volatiles of 4 sweet orange oils were characterized by descriptive sensory analysis and principal component analysis.…”

Assessment of genetic diversity of Saraca asoca (Roxb.) De Wilde: a commercially important, but endangered, forest tree species in Western Ghats, India

“…Most importantly, it provides much valuable information on the population genetic parameters required by foresters and conservationists, despite certain drawbacks like problems with production of reproducible fingerprints. This technique is widely used to study plant populations at species and cultivar levels because it is simple to perform, rapid, cost-effective and does not require prior knowledge of DNA sequences (Lamine and Mliki 2015;Mucciarelli et al 2015;Pendkar et al 2016).…”

An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers

“…These include random amplified polymorphic DNA (RAPD) (Williams et al, 1990;Hess et al, 2000;Lima et al, 2011;Kumla et al, 2012;Fu et al, 2000Fu et al, , 2013Shakeel et al, 2013;Lamine and Mliki, 2015), internal transcribed spacer (Hess et al, 2000;Varela et al, 2004;Pachuau et al, 2014), simple sequence repeat (Noormohammadi et al, 2013;Lamine and Mliki, 2015), inter-simple sequence repeat (ISSR) (Noormohammadi et al, 2013;Khadivi-Khub and Soorni, 2014), inter-retrotransposon amplified polymorphism (Noormohammadi et al, 2013), single primer amplification reaction (Satish et al, 2016), amplified fragment length polymorphism (Vos et al, 1995;Han et al, 2007;Khadivi-Khub and Soorni, 2014), and restriction fragment length polymorphism (Jeffreys et al, 1985;Tanksley et al, 1989) techniques. These techniques have been applied widely to various unicellular and multicellular organisms across different research areas.…”