Genetic variation of some Thai rice cultivars detected by random amplified polymorphic DNA analysis

Abstract

Random amplified polymorphic DNA (RAPD) was used to examine genetic variation of 10 Thai rice cultivars; of which Khao Dawk Mali 105, Khao Tah Haeng 17, Leuang Pratew123, Look Daeng Pattani and Gow Ruang 88 are salt tolerant, Muey Nawng 62 M, Nahng Pa-yah 132, Yah Yaw, Foi Tawng and Leb Nok Pattani are salt sensitive cultivars, comparing to 2 exotic cultivars: Pokkali, a salt tolerant rice of Sri Lanka and IR 28, a salt sensitive cultivar from the International Rice Research Institute. When twenty 10 nucleotide-long random primers were used to amplify total genomic DNA from 6 rice cultivars, five primers: provided 16-31 polymorphic DNAs that can identify individual cultivar. Primer X9 (ACGGCCGACC) gave the highest polymorphism. The similarity coefficient (SC) ranging from 0.09-0.58 was obtained among 6 cultivars with 5 primers. The dendrogram revealed by UPGMA cluster analysis classified 6 cultivars into 2 groups. PrimerX9 has the highest tendency to distinguish salt tolerant cultivars from salt sensitive cultivars, because the 5 salt tolerant nee cultivars were separated from IR 28, showing the highest genetic diversity between IR 28 and Pokkali. When all 12 cultivars were used to analyze genetic variation by primer X9, the dendrogram constructed from similarity coefficient separated 10 Thai rice cultivars from 2 exotic rice cultivars: Pokkali and IR 28 by 600 bp DNA band as molecular marker. Analysis of similarity coefficient indicated that the 5 salt tolerant Thai cultivars from all regions: Gow Ruang 88, Look Daeng Pattani, Leuang Pratew 123, Khao Dawk Mali 105 and Khao Tah Haeng 17 are most closely related (SC 0.75-0.93), whereas the 4 salt sensitive cultivars from the South: Nahng Pa-yah 132,Yah Yaw, Foi Tawng and Leb Nok Pattani showed SC: 0.75-0.80. From eight phenological indices of salt tolerance: percent germination, leaf damage, plant height, tillering, ratio of shoot/root dry weight, panicles/ plant, filled grains/ panicle and 100-grain weight, the results showed that leaf damage is the best criterion for distinguishing salt tolerant cultivars with lower leaf damage (10.74-21.87 %) significantly from salt sensitive cultivars (39.37-49.43%), and this phenological index showed good correlation with the genetic similarity analyzed by RAPD (SC 0.75-0.93). At the salt concentration of 8 dS/m, Khao Tah Haeng 17 showed the lowest leaf damage, while MN 62M was the most salt sensitive cultivar in the vegetative phase.