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.