Molecular Systematics of Eastern Cottonwood Using AFLP and RAPD Markers.

Abstract

Eastern cottonwood (Populus deltoides Bartr.) is the fastest growing tree in southeastern United States with great potential as a biomass source. DNA-based molecular marker techniques are playing increasingly important roles in elucidating genetic diversity within species. Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were employed to study genetic relationships among 57 clones from subregion Lower Mississippi river, West Central, and West Gulf. A total of 101 polymorphic RAPD markers were amplified from 14 primers. Six AFLP primer pairs resulted in a total of 457 polymorphic markers. Both RAPD and AFLP markers were able to uniquely identify all clones, indicating that extensive genetic diversity existed among the clones and demonstrating their efficiency as fingerprinting tools. To understand population structure in eastern cottonwood, leaf samples from 202 trees involving 12 natural populations from subregion East Central, East Gulf, and South Atlantic along the species' geographic regions were collected. All identified polymorphic markers, including 492 AFLP markers and 104 RAPD markers were included in the analysis. The within-population genetic diversity was estimated to be 0.2543 from AFLP data and 0.2619 from RAPD data, suggesting there is significant genetic variation within populations. The coefficient of gene differentiation among populations (FST) was estimated to be 0.0663 and 0.0536 for AFLP and RAPID respectively (P < 0.001), suggesting population subdivision in eastern cottonwood. The correlation between AFLP and RAPID data matrices based on Nei's standard genetic distance as measured by Pearson product moment correlation was 0.4251 (P = 0.027). Phylogenetic trees were constructed by UPGMA and Neighbor joining method. From AFLP data, populations from East Gulf were always grouped together in both trees and this was further supported by bootstrap test of significance of the trees. The UPGMA tree from RAPD suggested populations from East Central and East Gulf are close to populations within the same subregion, whereas the Neighbor-joining tree supported populations from East Central are grouped together. In addition, the variances associated with the population parameters from AFLP analysis were significant lower than that from RAPD analysis, suggesting AFLP analysis is a more reliable tool than RAPD analysis for population study.