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Research articles

ScienceAsia 45 (2019): 309-317 |doi: 10.2306/scienceasia1513-1874.2019.45.309

Evaluating sugarcane genotypes for genetic variation with differential sucrose accumulation using TRAP markers and partial Sai nucleotide polymorphism

Trin Srivonga, Yun J. Zhub, Suchirat Sakuanrungsirikulc, Chifumi Nagaib, Manit Kosittrakuna,*

ABSTRACT:     This study was conducted to characterize 17 sugarcane genotypes from Hawaii and Thailand using 12 target region amplification polymorphism (TRAP) markers and partial Sai nucleotide polymorphism. A total of 275 fragments were produced, of which 273 (99.27%) were polymorphic. The polymorphic information content (PIC) ranged from 0.912–0.959 with an average value of 0.938. Genetic similarity (GS) by Dice’s similarity coefficient ranged from 0.19–0.81 with a mean of 0.44. The 14 sugarcane genotypes from the Thailand collection with different sugar content were also assessed. A total of 198 fragments were found, of which 174 (87.88%) were polymorphic. The PIC value ranged from 0.860–0.937 with an average value of 0.914. The GS ranged from 0.49–0.85 with a mean of 0.71. The dendrograms constructed by the UPGMA cluster indicate strong differentiation between the Thai sugarcane genotypes and the Hawaiian sugarcane genotypes. In addition, S. officinarum is the group most closely associated with modern sugarcane. The partial Sai nucleotide sequence of 16 sugarcane genotypes from Hawaii and Thailand comprised 608–692 bp, within exon 2. There were 49 single nucleotide polymorphisms (SNPs) and two sites of variation including insertion and deletion (In/Del). Sai nucleotide polymorphism data matrices produced a more refined phylogenetic tree that shows four distinct groups. The results derived from nucleotide sequencing were somewhat similar to those derived from the TRAP markers. Thus, the utilization of informative TRAP and Sai nucleotide sequencing for a genetic variation study can result in the selection of diverse sugarcane parents for trait of sucrose content.

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a Applied Taxonomic Research Center, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002 Thailand
b Hawaii Agriculture Research Center (HARC), Waipahu, HI 96797 USA
c Khon Kaen Field Crops Research Center, Department of Agriculture, Ministry of Agriculture and Cooperatives, Khon Kaen 40000 Thailand

* Corresponding author, E-mail: manit.kosittrakun@fulbrightmail.org

Received 31 Jul 2018, Accepted 6 Jul 2019