Rice Genome Research in Korea

Kim, Tae-ho PhD
Crop Genomics Laboratory
Department of Agricultural Biotechnology, Genomics Division
National Academy of Agricultural Science (NAAS)
Jeonju, Republic of Korea

The National Academy of Agricultural Science (NAAS) of Rural Development Administration was part of an international effort to sequence the Nipponbare genome, which has since served as a reference for rice genome sequencing and as an impetus for the advancement of three major rice research fields in Korea, quantitative trait locus (QTL) analysis using molecular markers, transcriptome analysis, and genomic resequencing. Rice breeders in Korea have developed a large number of genetic mapping populations, such as NIL (near isogenic lines) and RIL (recombinant inbred lines) for various QTLs. The National Academy of Agricultural Science (NAAS) has developed a web-based genetic marker system to provide information about SNP and QTL markers in rice, which allows users to access a detailed characterization table of 12,829 potential SNPs in 3,356 genes. The QTL marker database provides information on 175 QTL markers with 942 polymorphic markers on each of the 12 rice chromosomes. Users are assisted in tracing new structures of the chromosomes and gene positional functions through comparisons using specific SNP and QTL markers. Transcriptome analyses using microarray-based or RNA-Seq-based technologies have been used extensively to explore organ-specific genomic expression and genomic responses to environmental cues and stresses, which also have made it possible to determine the relationships between genes involved in various biological systems. To facilitate high-throughput gene expression analysis and easier exploration of publicly available transcriptome data, public web databases have been constructed through international and national co-operative efforts. Based on the reference Nipponbare sequence, many Korean rice varieties have been subjected comparative genomic analysis using NGS technology. Recently, whole-genome resequencing has demonstrated sequence diversity between five Korean rice accessions, including Korean elite varieties, Hwayeong and Dongjin. Currently, whole-genome resequencing has been used extensively to analyze many mapping populations. In the effort to accelerate the agricultural utility of genomic sequence information, the National Agricultural Biotechnology Information Center (NABIC) has reconstructed a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker, and gene annotation. The marker-based database provides useful information via a user-friendly web interface that assists in tracing new structures of the chromosomes and gene positional functions using specific molecular markers.

Major publications

Cao P, Jung K-H, Choi Ds, Hwang Dh, Zhu J and Ronald PC (2012) The rice oligonucleotide array database: An atlas of rice gene expression. Rice 5:17.

Huh SM, Hwang YS, Shin YS et al. (2013) Comparative transcriptome profiling of developing caryopses from two rice cultivars with differential dormancy. J. Plant Physiol 170(12):1090-100.

Jeong IS, Yoon UH, Lee GS et al. (2013) SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing. Rice 6(6):1-12.

Jung K-H, Ko H-J, Nguyen MX, Kim S-R, Ronald P, and An G (2012) Genome-wide identification and analysis of early heat stress responsive genes in rice J. Plant Biol. 55:458-468

Yoon UH, Lee Jeonghwa, Hahn JH, Kim YK, Lee GS, Ji HS, Kim CK, Mun JH, Kim YM and Kim TH (2012) Structural and expression analysis of prolamin genes in Oryza sativa L. Plant Biotechnology Report 6:251-262.

Kwon SJ, Cho YC, Kwon SW et al. (2008) QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.). Breeding science. 58:271-279.

Kim CK, Seol YJ, Lee DJ et al. (2013) NABIC marker database: A molecular markers information network of agricultural crops. Bioinformation 9(17): 887-888.

Kim CH, Kikuchi S, Kim YK et al. (2010) Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice. BioChip J. 4(3): 247-255.

Kim CK, Yoon UH, Lee GS et al. (2009) Rice genetic marker database: An identification of single nucleotide polymorphism (SNP) and Quantitative trait loci (QTL) markers. African J. of Biotechnology 8(13) 2963-2967.

Kim CK, Park DS, Seol YJ et al. (2012) A genome-based database for agricultural biotechnology. Scientific Research and Essays 7(11): 1256-1261.

Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M, Yoon UH, Nahm BH (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol. 151:16-33

Minh-Thu PT, Hwang DJ, Jeon JS, Nahm BH, Kim YK. (2013) Transcriptome analysis of leaf and root of rice seedling to acute dehydration. Rice 6:38

Databases

NABIC (http://nabic.rda.go.kr) provide access to bioinformatic databases of genomic researches of agricultural plants and microbes in Korea.

PlantArrayNet (http://arraynet.mju.ac.kr/arraynet/) is a new version of RiceArrayNet that correlates gene expression obtained from transcriptome profiling data and applies it to the analysis of coexpressed genes in rice.

Symposium of Rice Functional Genomics using Insertional Mutagenesis at the NAAS, Korea in 2010.

Front row: Prof. C.D. Hahn, Dr. S.C. Suh, Prof. B.H. Nam, Prof. G.H. An, Dr. K.Y. Jung, Prof. Y.D. Choi, Dr. Y.H. Kim, Prof. K.H. Jung, Dr. J.H. Hahn, Dr. B.S. Koo

Back row: Dr. D.S Park, Dr. M.O. Byun, Dr. J.Y. Lee, Dr. Y.K. Kim, Prof. K.H. Lee, Dr. S.C. Park, Dr. D.W. Yun, Prof. J.K. Kim, Dr. S.K. Park, Dr. B.S. Park, Dr. H.S. Ji, Dr. U.H. Yoon, Dr. S.J. Kwon, Dr. G.S. Lee