Rice Genomics in Taiwan

Yue-ie Caroline Hsing
Institute of Plant and Microbial Biology
Academia Sinica

The Rice Genome Project facilitates the rice crop breeding programs in Taiwan in two aspects, variety identification and marker-assisted selection (MAS). Variety identification is important to trace purity in three-step propagation nurseries and identify the authenticity of domestic varieties in rice market in Taiwan. MAS can promote breeding efficiency because of precise selection and reducing redundant progeny test in breeding programs, specifically in the strategies of backcross breeding method and gene pyramiding in Taiwan.

Approximate 20,000 simple sequence repeat (SSR) markers were mined and available from the supplementary data of IRGSP. A set of 23 markers which were identified to discriminate 22 elite rice cultivars cultivated in 2004 and 2005 were successfully applied to assess the genetic consistency of seeds produced under three-step propagation system and identify off-type rice plants. Genetic diversity of rice germplasm used in Taiwan breeding programs were evaluated by using SSR markers, revealing that genetic diversity of Taiwan cultivars was relatively narrow, specifically in japonica varieties. A panel of 32 SSRs was applied to adulteration tests for prevent fraudulent commercial rice in the market. The whole genome sequence of Nipponbare is available, which can serve as reference genome to mine single nucleotide polymorphism (SNPs) among different close-related varieties. A database was constructed to retrieve polymorphic SNPs with discrimination of Taiwanese elite cultivars.

Polymorphic SSRs and SNPs have been extensively applied to linkage analyses, mapping of quantitative trait loci (QTLs) and positional cloning. Functional markers or flanking markers corresponding to target traits are used for foreground selection, and distributed on chromosomes are used for background selection. Tainan 16, an elite japonica rice possessing premium grain quality for its crystal transparent grains and glossy and elastic cooked rice, is Taiwan’s first variety bred by MAS. It took only 5 years to release Tainan 16 since the most popular Japanese cultivar, Koshihikari, was crossed to Taiwanese cultivar, Tainung 67. Three functional markers of heading dates used as foreground selection and 87 SSRs used as background selection were executed the in backcross breeding program. MAS is also applied to salt and drought tolerance, and bacterial blight and blast resistance, and is turned to be a routine strategy in rice breeding programs in Taiwan.

List of Publications

Hsu YC, Tseng MC, Wu YP, Lin MY, Wei FJ, Hwu KK, Hsing YI, Lin YR (2014) Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross. Mol. Breed. 34: 655-673.

Hour ZY, Wu MT, Lu SH, Hsing YIC, Chen HM (2014) Beyond the cleavage products of small regulatory RNAs: unraveling the complexity of plant RNA degradome data. BMC Genomics 15: 15.

Cal AJ, Liu D, Mauleon R, Hsing YIC, Serraj R (2013) Transcriptome profiling of leaf elongation zone under drought in contrasting rice cultivars. PloS One 8: e54537.

Droc G, An G, Hsing YI, Hirochika H, Pereira A, Undaresan CS, Han CD, Upadhyaya N, Ramachandran S, Comai L, Leung H, Guiderdoni E (2013) Mutant resources for the functional analysis of the rice genome. In: Genetics and Genomics of Rice, R Wing and Q Zhang (eds). Springer. pp. 81-115.

Wei FJ, Droc G, Guiderdoni E, Hsing YI (2013) International Consortium of Rice Mutagenesis: resources and beyond. Rice 6:39.

Lin HY, Wu YP, Hour AL, Ho SW, Wei FJ, Hsing YI, Lin YR (2012) Genetic diversity of rice germplasm used in Taiwan breeding programs. Bot. Studies 53: 363-376.

Lin YR, Wu SC, Chen SE, Tseng TH, Chen CS, Kuo SC, Wu HP, Hsing YI (2011) Mapping of quantitative trait loci for plant height and heading date in two inter-subspecific crosses of rice and comparison across Oryza genus. Bot. Studies 52: 1-14

Chern CG, Fan MJ, Huang SC, Yu SM, Wei FJ, Wu CC, Trisiriroj A, Lai MH, YIC Hsing (2010) Methods for rice phenomics studies. In: Plant Reverse Genetics, Andy Pereira (ed.) Humana Press.

Delseny M, Han B, Hsing YI (2010) High throughput DNA sequencing: the new sequencing revolution. Plant Sci. 179: 407-422.

Krishnan A, Guiderdoni E, An G, Hsing YI, CD Han CD, Lee MC, Yu SM, Upadhyaya N, Ramachandran S, Zhang Q, Sundaresan V, Hirochika H, Leung H, Pereira A (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol. 149:165-70.

Huang MD, Wei FJ, Wu CC, Hsing YI, Huang AH (2009) Analyses of advanced rice anther transcriptomes reveal global tapetum secretory functions and potential proteins for lipid exine formation. Plant Physiol. 149:694-707.

Chou HH, Trisiriroj A, Park S, Hsing YI, Ronald PC, Schnable PS (2009) Direct calibration of PICKY-designed microarrays. BMC Bioinformatics 10:347.

Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-1033.

Meier S, Gehring C, MacPherson CM, Kaur M, Maqungo M, Reuben S, Muyanga S, Shih MD, Wei FJ, Wanchana, Mauleon R, Radovanovic A, Bruskiewich R, T Tanaka T, B Mohanty B, R Wing R, T Gojobori T, T Sasaki T, S Swarup S, YI Hsing YI, VB Bajic VB (2008) The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network. Rice 1: 177-187.

Lin YR, YP Wu, FJ Wei, PC Lu, YC Huang, CH Chang, AL Hour, SC Kou, JS Hsieh, YI Hsing (2008) Construction of the Website ‘The Resource of Rice Genetic Markers in Taiwan’. Crop, Environment & Bioinformatics 5: 1-21.

Lo SF, Yang SY, Chen KT, Hsing YI, Zeevaart JA, Chen LJ, Yu SM (2008) A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice. Plant Cell 20: 2603-18.

Lu CA , CC Lin , KW Lee , JL Chen , LF Huang , SL Ho , HJ Liu , YI Hsing , SM Yu . (2007) The SnRK1A protein kinase plays a key role in sugar signaling during germination and seedling growth of rice. Plant Cell 19: 2484-99.

Yu SM , SS Ko , CY Hong , HJ Sun , YI Hsing , CG Tong , TH Ho (2007) Global functional analyses of rice promoters by genomics approaches. Plant Mol Biol. 65: 417-425.

Hour AL, YC Lin, PF Li, TY Chow, WF Lu, FJ Wei, Hsing YI (2007) Detection of SNPs between Tainung 67 and Nipponbare rice cultivars. Bot. Studies 48: 243-253.

Hsing YI, CG Chern, MJ Fan et al. (2007) A Rice gene activation/knockout library for high throughput functional genomics analysis. Plant Mol Biol. l63: 351-364.

Chern CG et al. (2007) A rice phenomics study - phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population

Guiderdoni E, An G, Yu SM, Hsing YI, Wu C (2007) T-DNA insertion mutants as a resource for rice functional genomics. In: Rice Functional Genomics – Challenges, Progress and Prospects. Narayana Upadhyaya (ed.) Springer. pp 187-227.

Lin YR, TY Chow, M Luo, D Kudrna, CC, RA Wing, YIC Hsing (2006) Two highly representative rice BAC libraries of japonica cv Tainung 67, suitable for rice structural and functional genomic research. Plant Sci.170: 889-896.

Chao YT, CS Chen, HH Chen, TY Chow, MC Chung, JS Hsieh, YI Hsing, PF Lee, YR Lin, JF Shaw, CL Su, HP Wu, SM Yu (2005) Completing the decoding of rice chromosome 5. J. Genet. Mol. Biol. 16: 198-210.

Cheng CH, MC Chung, MM Liu, SK Chen, FY Kao, SJ Lin, SH Hsiao, IC Tseng, YIC Hsing, HP Wu, CS Chen, JF Shaw, JZ Wu, T Matsumoto, T Sasaki, HH Chen, TY Chow (2005) A fine physical map of the rice chromosome 5. Mol. Gen. Genomics 274:337-45.

Su CL, Chung CI, Lin YC, Lu PC, Wei FJ, Hsing YI, Hour AL (2005) Statistical analysis of rice SAGE data. J. Genet. Mol. Biol. 16: 248-260.

Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow TY, Hsing YI, Kitano, Yamaguchi I, Matsuoka M (2005) Gibberellin insensitive dwarf 1 encodes soluble receptor for gibberellin. Nature 437:693-698.

International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.