Sequence-related Amplified Polymorphism and Target Region Amplification Polymorphism Markers-based Profiling of Sodium Azide and Ethyl Methanesulfonate-derived Black Rot-resistant Dendrobium sp. ‘Earsakul’ Mutants from In Vitro Mutagenesis and Selection

Abstract

To reveal the applicability of sequence-related amplified polymorphism (SRAP) and target region amplification polymorphism (TRAP) markers to mutant genotyping and marker identification for resistance to black rot (Phytophthora palmivora) in orchids (Dendrobium sp. ‘Earsakul’), we fingerprinted four nonmutagenized controls and 12 black rot-resistant mutants obtained with in vitro sodium azide (NaN3) and ethyl methanesulfonate (EMS) mutagenesis and in vitro selection using culture filtrate of P. palmivora. Each of the 20 SRAP and TRAP primer combinations yielded 375 and 384 scorable DNA bands, respectively, of which 94 (24.42%) and 88 (22.91%) were polymorphic, respectively. Mantel’s test cophenetic correlation coefficients of SRAP, TRAP, and SRAP/TRAP were 0.750, 0.921, and 0.861, respectively, indicating the efficiency of these markers, especially TRAP and SRAP/TRAP, for Dendrobium sp. ‘Earsakul’ mutant characterization. Moreover, the correlations between the matrices of cophenetic correlation values for the dendrograms of SRAP with TRAP, SRAP with SRAP/TRAP, and TRAP with SRAP/TRAP were 0.399, 0.566, and 0.793, respectively, and the dendrograms based on SRAP vs. TRAP and SRAP vs. SRAP/TRAP, with lower correlations, had more variations, i.e., the number of clusters, the members of clusters, and the placement of the materials, than the ones based on TRAP vs. SRAP/TRAP. Among the three dendrograms, all nonmutagenized controls were clustered together, whereas all the highly resistant and the most resistant mutants were distributed separately as individuals. Interestingly, the four SRAP and TRAP markers were significantly associated with black rot resistance. Overall, our results will be useful for facilitating future Dendrobium sp. ‘Earsakul’ breeding programs.