Journal of Plant Biology

, Volume 61, Issue 2, pp 80–84 | Cite as

Comparative Analysis of Flanking Sequence Tags of T-DNA/Transposon Insertional Mutants and Genetic Variations of Fast-neutron Treated Mutants in Rice

  • Woo-Jong Hong
  • Ki-Hong Jung
Original Article


Whole genome sequencing analyses of 1,504 fast-neutron (FN)-induced mutants of ‘Kitaake’ rice variety have revealed a new mutant population covering 58.6% of transposable element (TE) genes and 47.6% of non-TE genes throughout the rice genome. Mutation rate for TE gene is much higher in FN-induced mutants (58.6%) than in flanking sequence tag (FST) population (25.7%), implying that the former are more randomly generated than the latter. By adding this resource to FST population, we found that the mutation rate for the rice genome increases from 53.1% to 78.1% and more importantly, the rate with multiple alleles increases from 35.2% to 56.1%. To test the functional significance of mutants produced by both FN-induction and T-DNA/transposon insertions, we analyzed the coverage of functionally characterized genes by using the Overview of functionally characterized Genes in Rice Online database (OGRO, These combined genetic resources cover the mutations for 90.9% of functionally characterized genes for morphological traits, 91.0% for physiological traits, and 92.6% for resistance or tolerance traits, indicating that a gene-indexed mutant population that includes FN-induced mutants is valuable to future research for improving most of the important agronomic traits.


Fast-neutron treated mutants Functional genomics Rice T-DNA/transposon insertional mutants Whole genome sequencing analyses 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12374_2017_425_MOESM1_ESM.xlsx (13 mb)
Supplementary material, approximately 13287 KB.


  1. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M (2012) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41: D991–D995CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB, Ries L, Dobbels AA, Campbell BW, Young NP, Anderson JE, Grant DM, Orf JH, Naeve SL, Muehlbauer GJ, Vance CP, Stupar RM (2014) Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 198: 967−981CrossRefPubMedCentralGoogle Scholar
  3. Chandran AKN, Lee G, Yoo Y, Yoon U, Ahn B, Yun D, Kim J, Choi H, An G, Kim T (2016) Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response. Rice 9: 17CrossRefPubMedPubMedCentralGoogle Scholar
  4. Eamens AL, Blanchard CL, Dennis ES, Upadhyaya NM (2004) A bidirectional gene trap construct suitable for T-DNA and Dsmediated insertional mutagenesis in rice (Oryza sativa L.). Plant Biotechnol J 2: 367−380CrossRefGoogle Scholar
  5. Hsing Y, Chern C, Fan M, Lu P, Chen K, Lo S, Sun P, Ho S, Lee K, Wang Y (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol 63: 351−364CrossRefGoogle Scholar
  6. Jeon J, Lee S, Jung K, Jun S, Jeong D, Lee J, Kim C, Jang S, Lee S, Yang K (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22: 561−570CrossRefGoogle Scholar
  7. Kim CM, Piao HL, Park SJ, Chon NS, Je BI, Sun B, Park SH, Park JY, Lee EJ, Kim MJ (2004) Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J 39: 252−263Google Scholar
  8. Klee H, Horsch R, Rogers S (1987) Agrobacterium-mediated plant transformation and its further applications to plant biology. Annu Rev Plant Biol 38: 467−486Google Scholar
  9. Kumar CS, Wing RA, Sundaresan V (2005) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J 44: 879−892CrossRefGoogle Scholar
  10. Li G, Chern M, Jain R, Martin JA, Schackwitz WS, Jiang L, Vega-Sánchez ME, Lipzen AM, Barry KW, Schmutz J (2016) Genomewide sequencing of 41 rice (Oryza sativa L.) mutated lines reveals diverse mutations induced by fast-neutron irradiation. Mol Plant 9: 1078−1081Google Scholar
  11. Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong PQ, Jones KC, Jiang L, Ruan D, Bauer D, Peng Y, Barry KW, Schmutz J, Ronald PC (2017) The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell 29: 1218−1231PubMedGoogle Scholar
  12. Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15: 1771−1780CrossRefPubMedCentralGoogle Scholar
  13. Sallaud C, Gay C, Larmande P, Bès M, Piffanelli P, Piégu B, Droc G, Regad F, Bourgeois E, Meynard D (2004) High throughput TDNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 39: 450−464CrossRefGoogle Scholar
  14. Tie W, Zhou F, Wang L, Xie W, Chen H, Li X, Lin Y (2012) Reasons for lower transformation efficiency in indica rice using Agrobacterium tumefaciens-mediated transformation: lessons from transformation assays and genome-wide expression profiling. Plant Mol Biol 78: 1−18CrossRefPubMedGoogle Scholar
  15. van Enckevort, L Ellen JG, Droc G, Piffanelli P, Greco R, Gagneur C, Weber C, González VM, Cabot P, Fornara F, Berri S (2005) EUOSTID: a collection of transposon insertional mutants for functional genomics in rice. Plant Mol Biol 59: 99−110PubMedGoogle Scholar
  16. Wang N, Long T, Yao W, Xiong L, Zhang Q, Wu C (2013) Mutant resources for the functional analysis of the rice genome. Mol Plant 6: 596−604PubMedGoogle Scholar
  17. Wei F, Droc G, Guiderdoni E, Yue-ie CH (2013) International consortium of rice mutagenesis: resources and beyond. Rice 6: 39CrossRefPubMedPubMedCentralGoogle Scholar
  18. Yamamoto E, Yonemaru J, Yamamoto T, Yano M (2012) OGRO: The Overview of functionally characterized Genes in Rice online database. Rice 5: 1−10CrossRefGoogle Scholar
  19. Zhang J, Li C, Wu C, Xiong L, Chen G, Zhang Q, Wang S (2006) RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res 34: D745−D748CrossRefPubMedGoogle Scholar
  20. Zhang Q, Li J, Xue Y, Han B, Deng XW (2008) Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant 1: 715−719Google Scholar

Copyright information

© Korean Society of Plant Biologists and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Graduate School of Biotechnology and Crop Biotech InstituteKyung Hee UniversityYonginKorea

Personalised recommendations