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Comparison of molecular genetic utilities of TD, AFLP, and MSAP among the accessions of japonica, indica, and Tongil of Oryza sativa L.

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Abstract

Rice is one of the most important food crops in the world. Genetic diversity is essential for cultivar improvement programs. We compared genetic diversity derived from insertion–deletion (in–del) or base substitutions by amplified fragment length polymorphism (AFLP), from transposon transposition mutations by transposon display (TD), and from cytosine methylation by methylation-sensitive amplified polymorphism (MSAP) in japonica, indica, and Tongil type varieties of Oryza sativa L. Polymorphic profiles from the three marker systems allowed us to clearly distinguish the three types of varieties. The indica type varieties showed the highest genetic diversity followed by the Tongil and japonica type varieties. Of the three marker systems, TD produced the highest marker indices, and AFLP and MSAP produced similar marker indices. Pair-wise comparisons of the three marker systems showed that the correlation between the two genetic markers systems (AFLP and TD, r = 0.959) was higher than the correlations between the genetic and epigenetic marker systems (AFLP and MSAP, r = 0.52; TD and MSAP, r = 0.505). Both genetic marker systems had similar levels of gene differentiation (G ST ) and gene flow (N m ), which differed in the epigenetic marker system. Although the G ST of the epigenetic marker system was lower than the genetic marker systems, the N m of the epigenetic marker system was higher than in the genetic marker systems, indicating that epigenetic variations have a greater influence than genetic variations among the O. sativa L. types.

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Acknowledgments

This work was funded by a grant from the Golden Seed Project, Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development of Korea (RDA), and the Korea Forest Service (Project number: ATIS-PJ00994003, FRIS-213001-04-3-SBA20), as well as a 2015 research grant from Kangwon National University (Grant No. 520159395). We also give our deepest appreciation to Dr. Kroshid Jena for his critical reading of and suggestions for this manuscript.

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    1. Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea

      Ji-Yeong Choi, Neha Samir Roy & Nam-Soo Kim

    2. Department of Agricultural Life Science, Kangwon National University, Chuncheon, 200-701, Korea

      Kyeong-Cheul Park

    3. Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 200-701, Korea

      Nam-Soo Kim

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    Choi, JY., Roy, N.S., Park, KC. et al. Comparison of molecular genetic utilities of TD, AFLP, and MSAP among the accessions of japonica, indica, and Tongil of Oryza sativa L.. Genes Genom 38, 819–830 (2016). https://doi.org/10.1007/s13258-016-0426-2

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