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Diversity Analysis of Japonica Rice using MITE-transposon Display  

Hong Seong-Mi (Chungnam National University)
Kwon Soo-Jin (National Institute of Agricultural Biotechnology (NIAB), RDA)
Oh Chang-Sik (Chungnam National University)
Wessler Susan R. (Department of Botany, University of Georgia)
Ahn Sang-Nag (Chungnam National University)
Publication Information
KOREAN JOURNAL OF CROP SCIENCE / v.51, no.3, 2006 , pp. 259-268 More about this Journal
Abstract
Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.
Keywords
miniature inverted transposable elements (MITE); amplified fragment length polymorphism (AFLP); transposon display (TD); mPing; terminal inverted repeat (TIR);
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