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PLOS ONE  2012 

Identification of Genome-Wide Variations among Three Elite Restorer Lines for Hybrid-Rice

DOI: 10.1371/journal.pone.0030952

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Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice.


[1]  Xie H, Luo J, Zhang S, Zheng J, Lin M, et al. (1994) Breeding of Restorer Lines in Indica Hybrid Rice. Hybrid Rice 3: 31–33.
[2]  Chen S (2000) Current Status and Prospect in the Development of Breeding Materials and Breeding Methodology of Hybrid Rice. Chinese Joural of Rice science 14: 165–169.
[3]  Wang Y, Li S, Li H, Gao K (2004) Breeding and Utilization of Restorer Line Shuhui 527 with Good Grain Quality and High Combining Ability in Grain Yield. Hybrid Rice 19: 12–14.
[4]  Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.
[5]  Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92.
[6]  Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5: 887–893.
[7]  Cronn R, Liston A, Parks M, Gernandt DS, Shen R, et al. (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research 36: e122.
[8]  Huang X, Feng Q, Qian Q, Zhao Q, Wang L, et al. (2009) High-throughput genotyping by whole-genome resequencing. Genome Research 19: 1068–1076.
[9]  Lai J, Li R, Xu X, Jin W, Xu M, et al. (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics 42: 1027–1030.
[10]  Huang X, Wei X, Sang T, Zhao Q, Feng Q, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: 961–967.
[11]  Liu S, Cheng H, Wang F, Zhu Y (2002) DNA Polymorphism of Main Restorer Lines of Hybrid Rice in China. Chinese Joural of Rice science 16: 1–5.
[12]  Duan S, Mao J, Zhu Y (2002) Genetic Variation of Main Restorer Lines of Hybrid Rice in China Was ReVealed by Microsatellite Markers. Acta Genetica Sinica 29: 250–254.
[13]  Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713–714.
[14]  Li R, Li Y, Fang X, Yang H, Wang J, et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124–1132.
[15]  Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution 24: 1596–1599.
[16]  Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L, et al. (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19: 55–64.
[17]  Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z-X, et al. (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial?inoculation. Proceedings of the National Academy of Sciences 95: 1663–1668.
[18]  Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, et al. (2006) The Broad-Spectrum Blast Resistance Gene Pi9 Encodes an NBS-LRR Protein and is a Member of a Multigene Family in Rice. Genetics: genetics.105.044891.
[19]  Song W-Y, Wang G-L, Chen L-L, Kim H-S, Pi L-Y, et al. (1995) A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21. Science 270: 1804–1806.
[20]  Sun X, Cao Y, Yang Z, Xu C, Li X, et al. (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37: 517–527.
[21]  Du B, Zhang W, Liu B, Hu J, Wei Z, et al. (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci U S A 106: 22163–22168.
[22]  Gao Z, Zeng D, Cui X, Zhou Y, Yan M, et al. (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Science China Life Sciences 46: 661–668.
[23]  Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, et al. (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40: 1023–1028.
[24]  Fan C, Xing Y, Mao H, Lu T, Han B, et al. (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112: 1164–1171.
[25]  Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, et al. (2005) Cytokinin oxidase regulates rice grain production. Science 309: 741–745.
[26]  Liu W, Wu C, Fu Y, Hu G, Si H, et al. (2009) Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice. Planta 230: 649–658.
[27]  Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39: 623–630.
[28]  Zhu Y, Nomura T, Xu Y, Zhang Y, Peng Y, et al. (2006) ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins in a Novel Deactivation Reaction in Rice. The Plant Cell 18: 442–456.
[29]  Wang Z, Zou Y, Li X, Zhang Q, Chen L, et al. (2006) Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing. The Plant Cell Online 18: 676–687.
[30]  Ahmadikhah A, Karlov GI (2006) Molecular mapping of the fertility-restoration gene Rf4 for WA-cytoplasmic male sterility in rice. Plant Breeding 125: 363–367.
[31]  Li R, Fan W, Tian G, Zhu H, He L, et al. (2009) The sequence and de novo assembly of the giant panda genome. Nature 463: 311–317.
[32]  Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60–65.
[33]  Tang Q, Feng M (2007) DPS Data processing system: Experimental design, statistical analysis, and data mining. Beijing: Science Press..
[34]  Zhao W, Wang J, He X, Huang X, Jiao Y, et al. (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Research 32: D377–D382.
[35]  Birney E (2004) GeneWise and Genomewise. Genome Research 14: 988–995.
[36]  Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883–887.
[37]  Feltus FA (2004) An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments. Genome Research 14: 1812–1819.


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