The assessment of genetic diversity of Castanea species by RAPD, AFLP, ISSR, and SSR markers

Abstract

Castanea Mill. (chestnut) is a multipurpose deciduous tree and member of the family Fagaceae, widely distributed throughout North America, Europe, and Asia. The evaluation of the genetic diversity of chestnut species is crucial for the effective conservation of this economically and ecologically valuable tree. In this study, we applied 4 DNA markers to detect the genetic variability among and within Castanea species and to compare the effectiveness of each system in estimating genetic variation. We amplified 106 random amplified polymorphic DNA (RAPD), 228 amplified fragment length polymorphism (AFLP), 42 intersimple sequence repeat (ISSR), and 36 simple sequence repeat (SSR) polymorphic markers using 12, 5, 4, and 5 primer combinations, respectively. The findings on the effective multiplex ratio, polymorphism information content, and marker index revealed that AFLP was the most effective molecular marker system used in this study. Each marker system classified the species under investigation into clear but incompletely separated clusters, although partial agreement was achieved with respect to species relationships when the RAPD method was employed. The comparison of the correlation coefficient of RAPD marker data and the other markers showed a higher correlation [(r = 0.69, P < 0.01), (r = 0.77, P < 0.01), and (r = 0.47, P < 0.01) with AFLP, ISSR, and SSR, respectively]. When variance was partitioned among and within groups, AFLP (94.62%) showed greater variation within the groups and reverse RAPD (67.87%) yielded greater variation among the groups. Overall, the results indicate that the AFLP represents an efficient molecular marker system for the assessment of chestnut genetic diversity and, hence, the development of effective conservation strategies to preserve this valuable tree species.

Detection of genetic variation in sandalwood using various DNA markers

“…This was also reflected by high correlation ( r = 0.96) between RAPD and ISSR analysis. High correlation values between two marker systems have been reported earlier in many plants species (Abdelhamid et al 2014 ). High correlation might be due to the fact that both molecular types are dominant markers and that each marker system samples a very small fraction of the genome that was arbitrarily amplified (Table 6 ).…”

Genetic diversity in Cola acuminata and Cola nitida using RAPD primers

“…ONOMO et al (2006) also reported polymorphism and intra-population variation in both C. acuminata and C. nitida germplasm in Cameroon using isoenzyme traits. DNA based molecular markers such as RAPDs have been reported to reveal genetic diversity in forest trees and crops (HEIDER et al, 2007;ABDELHAMID et al, 2014).…”

“…Polymerase Chain Reaction (PCR) based markers using arbitrary primers, such as Random Amplified Polymorphic DNA (RAPD), have been widely used for investigating genetic relatedness and diversity in plant populations and cultivars (LI and NELSON, 2001;PAREDES et al, 2002;SAINI et al, 2010;MUHAMMAD and MUHAMMAD, 2014;MILADINOVIĆ et al, 2018). Genetic discoveries can often provide novel, conservation-relevant insights and strategies (ABDELHAMID et al, 2014). ONOMO et al, (2006) reported isoenzyme variability germplasm of three species of Cola in Cameroon.…”

Genetic diversity of the Salix lapponum L. population intended as a source of material for reintroduction

“…These values were especially surprising in the light of the results described in the paper by Pogorzelec et al (2014c), where the genetic diversity obtained by ISSR markers between four populations located in the Łęczna-Włodawa Lakeland was twice smaller. The present Φ PT value may result from very high linkage disequilibrium of loci, which was especially high at the whole population level, and from applying the AFLP method whose results in many publications significantly differ from those obtained by ISSR (Abdelhamid et al, 2014;Badfar-Chaleshtori et al, 2012;Chen et al, 2010;Khadivi-Khub & Soorni, 2014). Despite that S. lapponum seeds are wind dispersed, they are usually deposited close to the parent plant due to the specific structure of the phytocenosis at the studied site (Pogorzelec et al, 2014b).…”