Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Analysis of germinating seed stage expressed sequence tags in Oryza sativa L.

벼 발아종자 발현유전자의 발현특성분석

  • Yoon, Ung-Han (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Lee, Gang-Seob (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Kim, Chang-Kug (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Lee, Jung-Sook (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Hahn, Jang-Ho (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Yun, Doh-Won (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Ji, Hyeon-So (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Lee, Tae-Ho (Bioscience and Bioinformatics Division, MyongJi University) ;
  • Lee, Jeong-Hwa (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Park, Sung-Han (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Kim, Gun-Wook (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Seo, Mi-Suk (Genomics Division, National Academy of Agricultural Science, RDA) ;
  • Kim, Yong-Hwan (Genomics Division, National Academy of Agricultural Science, RDA)
  • Published : 2009.09.30
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Abstract

Seed germination is the important stage to express many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mechanisms, we were analyzed the rice cDNA clones (Oryzasativa cultivar Ilpum) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,66 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as commonly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages. For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.

Keywords

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