水稻重组自交系的基因型鉴定及栽培稻和药用野生稻基因组序列比较分析
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摘要
随着生物技术的发展,第二代测序技术的开发填补了很多传统生物学方法的不足。不断新增的基因组序列,为重新设计基因型鉴定战略,进行更有效的遗传图谱构建和基因组分析创造了机会。本研究中我们首次利用Solexa高通量基因组分析系统,开发了一种使用bar-coding的测序方法,通过获得低覆盖率的水稻全基因组序列对重组自交系进行基因型的鉴定。我们通过检测150个重组自交系个体的低覆盖率全基因组序列与亲本之间的单核苷酸多态性,设计了一种滑动窗口的方法,检测出每个个体在全基因组范围内的基因型分布和重组断点,分析并鉴定它们的基因型。利用这种方法,我们共构建了150个水稻重组自交系的遗传图,基因型分布的准确率达到99.94%,重组断点的分辨率为平均每40kb存在一个重组断点。相比我们之前利用287个遗传标记,基于传统的PCR扩增方法构建得到的水稻遗传图,Solexa高通量测序方法在数据的获取效率和鉴定重组断点的精确度方面分别提高了20倍和35倍。用基于全基因组测序方法构建的遗传图谱,成功地将水稻第一号染色体上一个控制植株高度性状的数量性状基因定位在100 kb区域范围内。通过计算机模拟,可以证明基于全基因组测序的基因型鉴定方法对各种生物群体的遗传作图都很适用,而且也可用于对较大的基因组和较低遗传多态性的生物物种进行鉴定与分析。随着测序技术的不断发展与革新,这种基于全基因组测序的基因型鉴定方法将有可能取代传统的基于遗传标记的PCR扩增方法,成为大规模发掘基因和解决各种生物学问题的一个强有力的工具。
植物近缘物种之间的基因组结构和序列比较分析可以为研究植物基因功能和进化提供参考。本研究中我们对水稻药用野生稻Oryza officinalis(CC基因组型)103,844个BAC末端序列(相当于~73.8 Mb的基因组序列长度)进行了分析;并比较了CC基因组与水稻栽培稻粳稻日本晴基因组(AA基因组型)的结构特征,发现45%以上的O.officinalis基因组序列是由重复序列构成的,高于水稻栽培稻粳稻日本晴重复序列所占的比例(~38.87%)。为了进一步了解AA基因组和CC基因组在结构上的差异,包括它们在基因的结构特征以及基因组大小(genome size)上的差异,我们选择了AA和CC基因组两个共线性区段中的BAC重叠群进行精确测序,结果表明:在AA基因组共线性区段预测分析得到的57个基因中,有39个基因与CC基因组是同源基因;通过共线性区段的比对还发现CC基因组在基因内和基因间隔区通过转座子插入等方式使其基因组发生了膨胀,基因组大小比AA基因组偏大。特别是反转座子的插入在CC基因组中尤为突出,分析结果显示CC基因组和AA基因组中的RNA转座元件的分别占17.95%和1.78%,这就解释了为什么在共线性区段CC基因组相比AA基因组多出了近100 kb的主要原因。
With the development of biotechnology, the next-generation sequencing technology makes up the shortage of conventional biological methods. The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have firstly developed a bar-coding sequencing strategy and a high-throughput genotyping method for recombinant populations by using Illumina Genome Analyzer to generate low coverage of rice whole genome sequences. By detecting SNPs between the RILs and their parents, we designed a sliding window approach to collectively examine genome-wide single nucleotide polymorphisms (SNPs) for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20 times faster in data collection and 35 times more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100 kb region containing the rice‘green revolution’gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and feasible for organisms with large genome sizes and low polymorphisms. With continuous improvement of sequencing technologies, this genome-based method may replace the traditional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated ~73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences of rice cultivar, O. sativa ssp. japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.
植物近缘物种之间的基因组结构和序列比较分析可以为研究植物基因功能和进化提供参考。本研究中我们对水稻药用野生稻Oryza officinalis(CC基因组型)103,844个BAC末端序列(相当于~73.8 Mb的基因组序列长度)进行了分析;并比较了CC基因组与水稻栽培稻粳稻日本晴基因组(AA基因组型)的结构特征,发现45%以上的O.officinalis基因组序列是由重复序列构成的,高于水稻栽培稻粳稻日本晴重复序列所占的比例(~38.87%)。为了进一步了解AA基因组和CC基因组在结构上的差异,包括它们在基因的结构特征以及基因组大小(genome size)上的差异,我们选择了AA和CC基因组两个共线性区段中的BAC重叠群进行精确测序,结果表明:在AA基因组共线性区段预测分析得到的57个基因中,有39个基因与CC基因组是同源基因;通过共线性区段的比对还发现CC基因组在基因内和基因间隔区通过转座子插入等方式使其基因组发生了膨胀,基因组大小比AA基因组偏大。特别是反转座子的插入在CC基因组中尤为突出,分析结果显示CC基因组和AA基因组中的RNA转座元件的分别占17.95%和1.78%,这就解释了为什么在共线性区段CC基因组相比AA基因组多出了近100 kb的主要原因。
With the development of biotechnology, the next-generation sequencing technology makes up the shortage of conventional biological methods. The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have firstly developed a bar-coding sequencing strategy and a high-throughput genotyping method for recombinant populations by using Illumina Genome Analyzer to generate low coverage of rice whole genome sequences. By detecting SNPs between the RILs and their parents, we designed a sliding window approach to collectively examine genome-wide single nucleotide polymorphisms (SNPs) for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20 times faster in data collection and 35 times more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100 kb region containing the rice‘green revolution’gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and feasible for organisms with large genome sizes and low polymorphisms. With continuous improvement of sequencing technologies, this genome-based method may replace the traditional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated ~73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences of rice cultivar, O. sativa ssp. japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.
引文
1 Wu, W.R., Li, W.M., Lu, H.R. (1997). Number of selfings required to produce a population of recombinant inbred lines. Journal of Fujian Agricultural University. 26(2): 129-132.
2 Li, S.S., Chen, M.X., Wang, H.G. (2001). Genetic analysis on qualitative-quantitative traits by using populations of recombinant inbred lines (RILs)——genetic models and inheritance of yield traits in wheat. Acta Agronomica Sinica. 27(6): 896-904.
3 Li, L., Yang, J.B., Mackill, D.J., Colowit, P.M. (2000). Application of automated fluorescent-labelled system for SSLPs analysis of different rice genotypes. Acta Agronomica Sinica. 26(5): 565-569.
4 Litt, M., Luty, J.A. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 44: 397-401.
5 Tautz, D. (1989). Hypervariability of simple sequence as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463-6471.
6 Weber, J.L., May, P.E. (1989). Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 44(3): 388-396.
7 Rafalski, J.A., Vogel, J.M., Morgante, M., Powell, W., Andre, C., and Tingey, S.V., (1996). Generating and using DNA markers in plants, In: Birren, B., Lai, E. (Eds.)., Nonmammalian genomic analysis: a practical guide. Academic Press. USA, pp.75-134.
8 Ribaut, J.M., and Hoisington, D. (1998). Marker-assisted selection: New tools and strategies. Trends in Plant Science. 3(6): 236-239.
9 Alderborn, A., Kristofferson, A., Hammerling, U. (2000). Determination of single nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res.10: 1249-1258.
10 Ronaghi, M., Uhlen, M., Nyren, P. (1998). A sequencing method based on realtime pyrophosphate. Science. 281: 363-365.
11 Ronaghi, M. (2001). Pyrosequencing sheds light on DNA sequencing. Genome Res. 11: 3-11.
12 Tsuchihashi, Z., Dracopoli, N.C. (2002). Progress in high throughput SNP genotyping methods. The Pharmacogenomics Journal. 2: 103-110.
13 Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. (2000). Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 28: 3752-3761.
14 Whitcombe, D., Theaker, J., Guy, S., Brown, T., Little, S. (1999). Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17: 804-807.
15 Chen, X., Levine, L., PY, K. (1999). Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9: 492-498.
16 Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., and Fodor, S-P.A. (1994). Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA. 91: 5022-5026.
17 Southern, E., Maskos, U., and Elder, J. (1993). Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 13: 1008-1017.
18 Wang, D.G., Fan, J.B., Siao, C-J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M.S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T.J., Lipshutz, R.J, Chee, M., and Lander, E.S. (1998). Large-scale identification, mapping, and genotyping of single nucleotide polymorphisms in the human genome. Science. 280: 1077-1082.
19 Fan, J.B., Chen, X.Q., Halushka, M.K., Berno, A., Huang, X.H., Ryder, T., Lipshutz,R.J., Lockhart, D.J., and Chakravarti, A. (2000). Parallel genotyping of human SNPs using generic high density oligonucleotide tag arrays. Genome Res. 10: 853-860.
20 Hirschhora, J.N., Sklar, P., Lindblad-Toh, K., Lim, Y.M., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E., and Lander, E.S. (2000). SBE-TAGS: an array-based method for efficient single nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA. 97: 12164-12169.
21 Winzeler, E.A., Richards, D.R., Conway, A.R., Goldstein, A.L., Kalman, S., McCullough, M.J., McCusker, J.H., Stevens, D.A., Wodicka, L., Lockhart, D.J., and Davis, R.W. (1998). Direct allelic variation scanning of the yeast genome. Science. 281: 1194-1197.
22 Meaburn, E., Butcher, L.M., Schalkwyk, L.C., and Plomin, R. (2006). Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucleic Acids Res. 34(4): e28.
23 Singer, T., Fan, Y.P., Chang, H.S., Zhu, T., Hazen, S.P., and Briggs, S.P. (2006). A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization. PLoS Genetics. 2: 1352-1361.
24 Edwards, J.D., Janda, J., Sweeney, M.T., Gaikwad, A.B., Liu, B., Leung, H., Galbraith, D.W. (2008). Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. Plant Methods. 4: 13.
25 Craig, D.W., Pearson, J.V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J.J., Pawlowski, T.L., Laub, T., Nunn, G., Stephan, D.A., Homer, N., Huentelman, M.J., (2008). Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods. 5(10): 887-893.
26 Cronn, R., Liston, A., Parks, M., Gernandt, D.S., Shen, R., and Mockler, T. (2008). Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36(19): e122.
27 Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads andcalling variants using mapping quality scores. Genome Res. 18: 1851-1858.
28 International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature. 436: 793-800.
29 Yu, J.,Wang, J., Lin,W., Li, S.G., Li, H., Zhou, J., Ni, P.X., Dong,W., Hu, S.N., Zeng, C.Q., Zhang, J.G., Zhang, Y., Li, R.Q., Xu, Z.Y., Li, S.T., Li, X.R., Zheng, H.K., Cong, L.J., Lin, L., Yin, J.N., Geng, J.N., Li, G.Y., Shi, J.P., Liu, J., Lv, H., Li, J., Wang, J., Deng, Y.J., Ran, L.H., Shi, X.L., Wang, X.Y., Wu, Q.F., Li, C.F., Ren, X.Y., Wang, J.Q., Wang, X.L., Li, D.W., Liu, D.Y., Zhang, X.W., Ji, Z.D., Zhao, W.M., Sun, Y.Q., Zhang, Z.P., Bao, J.Y., Han, Y.J., Dong, L.L., Ji, J., Chen, P., Wu, S.M., Liu, J.S., Xiao, Y., Bu, D.B., Tan, J.L., Yang, L., Ye, C., Zhang, J.F., Xu, J.Y., Zhou, Y., Yu, Y.P., Zhang, B., Zhuang, S.L., Wei, H.B., Liu, B., Lei, M., Yu, H., Li, Y.Z., Xu, H., Wei, S.L., He, X.M., Fang, L.J., Zhang, Z.J., Zhang, Y.Z., Huang, X.G., Su, Z.X., Tong, W., Li, J.H., Tong, Z.Z., Li, S.L., Ye, J., Wang, L.S., Fang, L., Lei, T.T., Chen, C., Chen, H., Xu, Z., Li, H.H., Huang, H.Y., Zhang, F., Xu, H.Y., Li, N., Zhao, C.F., Li, S.T., Dong, L.J., Huang, Y.Q., Li, L., Xi, Y., Qi, Q.H., Li, W.J., Zhang, B., Hu, W., Zhang, Y.L., Tian, X.J., Jiao, Y.Z., Liang, X.H., Jin, J., Gao, L., Zheng, W.M., Hao, B.L., Liu, S.Q., Wang, W., Yuan, L.P., Cao, M.L., McDermott, J., Samudrala, R., Wang, J., Wong, G.K., Yang, H. (2005). The genomes of Oryza sativa: A history of duplications. PLoS Biol. 3(2): 266-281.
30 Dohm, J.C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36(16): e105.
31 Van Os, H., Andrzejewski, S., Bakker, E., Barrena, I., Bryan, G.J., Caromel, B., Ghareeb, B., Isidore, E., de Jong, W., van Koert, P., Lefebvre, V. Milbourne, D. Ritter, E. van der Voort, J.N-A-M.R. Rousselle-Bourgeois, F. van Vliet, J. Waugh, R. Visser, R.G-F. Bakker, J. van Eck, H.J. (2006). Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated geneisolation and a genomewide physical map. Genetics. 173: 1075-1087.
32 Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G.S., et al. (2002). Green revolution: A mutant gibberellin-synthesis gene in rice. Nature. 416: 701-702.
33 Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H., and Turner, D.J. (2008). A large genome center’s improvements to the Illumina sequencing system. Nat. Methods. 5(12): 1005-1010.
34 Bennetzen, J.L. (2007). Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10: 176-181.
35 Tang, H.B., Bowers, J.E., Wang, X.Y., Ming, R., Alam, M., and Paterson, A.H. (2008). Synteny and collinearity in plant genomes. Science. 320: 486-488.
36 Sasaki, T., and Burr, B. (2000). International rice genome sequencing project: the effort to completely sequence the rice genome. Curr. Opin. Plant Biol. 3: 138-141.
37 Yu, J., et al. A draft sequence of the rrice genome (Oryza sativa L. ssp. indica). (2002). Science. 296: 79-92.
38 Feng, Q., Zhang, Y.J., Hao, P., Wang, S.Y., Fu, G., Huang, Y.C., Li, Y., Zhu, J.J., Liu, Y.L., Hu, X., Jia, P.X., Zhang, Y., Zhao, Q., Ying, K., Yu, S.L., Tang, Y.S., Weng, Q.J., Zhang, L., Lu, Y., Mu, J., Ku, Y.Q., Zhang, L-S., Yu, Z., Fan, D.L., Liu, X.H., Lu, T.T., Li, C., Wu, Y.R., Sun, T.G., Lei, H.Y., Li, T., Hu, H., Guan, J.P., Wu, M., Zhang, R.Q., Zhou, B., Chen, Z.H., Chen, L., Jin, Z.Q., Wang, R., Yin, H.F., Cai, Z., Ren, S.X., Lv, G., Gu, W.Y., Zhu, G.F., Tu, Y.F., Jia, J., Zhang, Y., Chen, J., Kang, H., Chen, X.Y., Shao, C.Y., Sun, Y., Hu, Q.P., Zhang, X.L., Zhang, W., Wang, L.J., Ding, C.W., Sheng, H.H., Gu, J.L., Chen, S.T., Ni, L., Zhu, F.H., Chen, W., Lan, L.F., Lai, Y., Cheng, Z.K., Gu, M.H., Jiang, J.M., Li, J.Y., Hong, G.F., Xue, Y.B., and Han, B. (2002). Sequence and analysis of rice chromosome 4. Nature. 420: 316-320.
39 International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature. 436: 793-800.
40 Ammiraju, J-S.S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A.C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C.Z., Goicoechea, J.T., Zuccolo, A., Chen, J.F., Bennetzen, J.L., Chen, M.S., Jackson, S.A., and Wing, R.A. (2008). Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell. 20: 3191-3209.
41 Vaughan, D.A. (1994). Wild relatives of rice: genetic resources handbook. (International Rice Research Institute, Manila, Philippines).
42 Aggarwal, R.K., Brar, D.S., and Khush, G.S. (1997). Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol. Gen. Genet. 254: 1-12.
43 Khush, G.S. (1997). Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35: 25-34.
44 Ge, S., Sang, T., Lu, B.R., and Hong, D.Y. (1999). Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA. 96: 14400-14405.
45 Ammiraju, J-S.S., Luo, M.Z., Goicoechea, J.L., Wang, W.M., Kudrna, D., et al. (2006). The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Research. 16:140-147.
46 Wing, R.A., Ammiraju, J-S.S., Luo, M.Z., Kim, H., Yu, Y., Kudrna, D., Goicoechea, J.L., Wang, W.M., Nelson, W., Rao, K., Brar, D., Mackill, D.J., Han, B., Soderlund, C., Stein, L., SanMiguel, P., and Jackson, S.A. (2005). The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. 59: 53-62.
47 FRARY, A., DOúANLAR, S. (2003). Comparative genetics of crop plant domestication and evolution. Turk. J. Agric. For. 27: 59-69.
48 Morishima, H. (2001). Evolution and domestication of rice. In Rice Genetics IV. Proc.of 4th Intern. Rice Genet. Symp. Edited by Khush, G.S., Brar, D.S., Hardy, B. New Delhi: Science Publishers, Inc: 63-77.
49 Tian, C.G., Xiong, Y.Q., Liu, T.Y., Sun, S.H., Chen, L.B., and Chen, M.S. (2005). Evidence for an ancient whole-genome duplication event in rice and other cereals. Acta Genetica Sinica. 32(5): 519-527.
50 Zou, X.H., Zhang, F.M., Zhang, J.G., Zang, L.L., Tang, L., Wang, J., Sang, T., and Ge, S. (2008). Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol. 9: R49.1-13.
51 Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J.C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.T., Stein, L., Ware, D., Jackson, S.A., Soderlund, C., and Wing, R.A. (2008). Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol. 9: R45.1-15.
52 Arumuganathan, K., and Earle, E.D. (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9(3): 208-218.
53 Piegu, B., Guyot, R., Picault, N., Roulin, A., Saniyal, A., Kim, H., Collura, K., Brar, D.S., Jackson, S.A., Wing, R.A., and Panaud, O. (2006). Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16: 1262-1269.
54 Ammiraju, J-S.S., Zuccolo, A., Yu, Y., Song, X., Piegu, B., Chevalier, F., Walling, J.G., Ma, J.X., Talag, J., Brar, D.S., SanMiguel, P., Jiang, N., Jackson, S.A., Panaud, O., and Wing, R.A. (2007). Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52: 342-351.
55 Kim, H., SanMiguel, P., Nelson, W., Collura, K., Wissotski, M., Walling, J.G., Kim, J.P., Jackson, S.A., Soderlund, C., and Wing, R.A. (2007). Comparative physical mapping between O. sativa (AA genome type) and O. punctata (BB genome type).Genetics. 176: 379-390.
56 Ma, J.X., Wing, R.A., Bennetzen, J.L., and Jackson, S.A. (2007). Evolutionary history and positional shift of a rice centromere. Genetics. 177: 1217-1220.
57 Zhang, S.B., Gu, Y.Q., Singh, J., Coleman-Derr, D., Brar, D.S., Jiang, N., and Lemaux, P.G. (2007). New insights into Oryza genome evolution: High gene colinearity and differential retrotransposon amplification. Plant Mol. Biol. 64: 589-600.
58 Lu, F., Ammiraju, J-S.S., Sanyal, A., Zhang, S.L., Song, R.T., Chen, J.F., Li, G.S., Sui, Y., Song, X., Cheng, Z.K., de Oliveira, A.C., Bennetzen, J.L., Jackson, S.A., Wing, R.A., and Chen, M.S. (2009). Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc. Natl. Acad. Sci. USA. 106: 2071-2076.
59 Mao L., Wood T.C., Yu Y., Budiman M.A., Tomkins J., Woo S-S., Sasinowski M., Presting G., Frisch D., Goff S., Dean R.A., and Wing, R.A. (2000). Rice transposable elements: A survey of 73,000 Sequence-Tagged-Connectors. Genome Res. 10: 982-990.
60 Bruggmann, R., Bharti, A.K., Gundlach, H., Lai, J.S., Young, S., Pontaroli, A.C., Wei, F.S., Haberer, G., Fuks, G., Du, C.G., Raymond, C., Estep, M.C., Liu, R.Y., Bennetzen, J.L., Chan, A.P., Rabinowicz, P.D., Quackenbush, J., Barbazuk, W.B., Wing, R.A., Birren, B., Nusbaum, C., Rounsley, S., Mayer, K.F-X., and Messing, J. (2006). Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16: 1241-1251.
61 Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A.K., and Khurana, J.P. (2007). F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143: 1467-1483.
62 Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A.,Pachter, L.S., and Dubchak, I. (2000). VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 16: 1046-1047.
63 Huang, X.H., Lu, G.J., Zhao, Q., Liu, X.H., and Han, B. (2008). Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 148: 25-40.
64 Gaut, B.S., Morton, B.R., McCaig, B.C., Clegg, M.T. (1996). Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA. 93: 10274-10279.
65 Yang, Z.H., and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.
66 Zhang, Z., Li, J., Zhao, X.Q., Wang, J., Wong, G.K-S., and Yu, J. (2006). KaKs Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 4: 259-263.
67 Heinrichs, E.A., Medrano, F.G., and Rapusas, H.R. (1985). Genetic evaluation for insect resistance in rice. IRRI.
68 Jena, K.K., Khush, G.S. (1989). Monosomic alien addition lines of rice: production, morphology, cytology and breeding behavior. Genome. 32: 449-455.
69 Jena, K.K., Khush, G.S. (1990). Introgressron of genes from Oryza officinalis Well ex Watt to cultivated rice, O.saliva L. Theor. Appl. Genet. 80: 737-745.
70章琦,王春莲,施爱农等. (1994).野生稻抗稻白叶枯病性(Xanthomonas oryzae pv. oryzae)的评价.中国农业科学. 27: 1-9.
71颜辉煌,程祝宽,刘国庆,陈纯贤,闵绍楷,朱立煌. (1999).栽培稻——药用野生稻杂种F1及回交后代的基因组原位杂交鉴定.遗传学报. 26 (2): 157-162.
72卢宝荣. (1998).稻种遗传资源多样性的开发利用及保护.生物多样性. 6: 63-72.
73 Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
74 Hass, B.L., Pires, J.C., Porter, R., Phillips, R.L., Jackson, S.A. (2003). Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theor. Appl. Genet. 107: 773-782.
75 Zhang, W.L., Yi, C.D., Bao, W.D., Liu, B., Cui, J.J., Yu, H.X., Cao, X.F., Gu, M.H., Liu, M., Cheng, Z.K. (2005). The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol. 139: 306-315.
2 Li, S.S., Chen, M.X., Wang, H.G. (2001). Genetic analysis on qualitative-quantitative traits by using populations of recombinant inbred lines (RILs)——genetic models and inheritance of yield traits in wheat. Acta Agronomica Sinica. 27(6): 896-904.
3 Li, L., Yang, J.B., Mackill, D.J., Colowit, P.M. (2000). Application of automated fluorescent-labelled system for SSLPs analysis of different rice genotypes. Acta Agronomica Sinica. 26(5): 565-569.
4 Litt, M., Luty, J.A. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 44: 397-401.
5 Tautz, D. (1989). Hypervariability of simple sequence as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463-6471.
6 Weber, J.L., May, P.E. (1989). Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 44(3): 388-396.
7 Rafalski, J.A., Vogel, J.M., Morgante, M., Powell, W., Andre, C., and Tingey, S.V., (1996). Generating and using DNA markers in plants, In: Birren, B., Lai, E. (Eds.)., Nonmammalian genomic analysis: a practical guide. Academic Press. USA, pp.75-134.
8 Ribaut, J.M., and Hoisington, D. (1998). Marker-assisted selection: New tools and strategies. Trends in Plant Science. 3(6): 236-239.
9 Alderborn, A., Kristofferson, A., Hammerling, U. (2000). Determination of single nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res.10: 1249-1258.
10 Ronaghi, M., Uhlen, M., Nyren, P. (1998). A sequencing method based on realtime pyrophosphate. Science. 281: 363-365.
11 Ronaghi, M. (2001). Pyrosequencing sheds light on DNA sequencing. Genome Res. 11: 3-11.
12 Tsuchihashi, Z., Dracopoli, N.C. (2002). Progress in high throughput SNP genotyping methods. The Pharmacogenomics Journal. 2: 103-110.
13 Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. (2000). Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 28: 3752-3761.
14 Whitcombe, D., Theaker, J., Guy, S., Brown, T., Little, S. (1999). Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17: 804-807.
15 Chen, X., Levine, L., PY, K. (1999). Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9: 492-498.
16 Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P., and Fodor, S-P.A. (1994). Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA. 91: 5022-5026.
17 Southern, E., Maskos, U., and Elder, J. (1993). Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 13: 1008-1017.
18 Wang, D.G., Fan, J.B., Siao, C-J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M.S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T.J., Lipshutz, R.J, Chee, M., and Lander, E.S. (1998). Large-scale identification, mapping, and genotyping of single nucleotide polymorphisms in the human genome. Science. 280: 1077-1082.
19 Fan, J.B., Chen, X.Q., Halushka, M.K., Berno, A., Huang, X.H., Ryder, T., Lipshutz,R.J., Lockhart, D.J., and Chakravarti, A. (2000). Parallel genotyping of human SNPs using generic high density oligonucleotide tag arrays. Genome Res. 10: 853-860.
20 Hirschhora, J.N., Sklar, P., Lindblad-Toh, K., Lim, Y.M., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E., and Lander, E.S. (2000). SBE-TAGS: an array-based method for efficient single nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA. 97: 12164-12169.
21 Winzeler, E.A., Richards, D.R., Conway, A.R., Goldstein, A.L., Kalman, S., McCullough, M.J., McCusker, J.H., Stevens, D.A., Wodicka, L., Lockhart, D.J., and Davis, R.W. (1998). Direct allelic variation scanning of the yeast genome. Science. 281: 1194-1197.
22 Meaburn, E., Butcher, L.M., Schalkwyk, L.C., and Plomin, R. (2006). Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucleic Acids Res. 34(4): e28.
23 Singer, T., Fan, Y.P., Chang, H.S., Zhu, T., Hazen, S.P., and Briggs, S.P. (2006). A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization. PLoS Genetics. 2: 1352-1361.
24 Edwards, J.D., Janda, J., Sweeney, M.T., Gaikwad, A.B., Liu, B., Leung, H., Galbraith, D.W. (2008). Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. Plant Methods. 4: 13.
25 Craig, D.W., Pearson, J.V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J.J., Pawlowski, T.L., Laub, T., Nunn, G., Stephan, D.A., Homer, N., Huentelman, M.J., (2008). Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods. 5(10): 887-893.
26 Cronn, R., Liston, A., Parks, M., Gernandt, D.S., Shen, R., and Mockler, T. (2008). Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36(19): e122.
27 Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads andcalling variants using mapping quality scores. Genome Res. 18: 1851-1858.
28 International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature. 436: 793-800.
29 Yu, J.,Wang, J., Lin,W., Li, S.G., Li, H., Zhou, J., Ni, P.X., Dong,W., Hu, S.N., Zeng, C.Q., Zhang, J.G., Zhang, Y., Li, R.Q., Xu, Z.Y., Li, S.T., Li, X.R., Zheng, H.K., Cong, L.J., Lin, L., Yin, J.N., Geng, J.N., Li, G.Y., Shi, J.P., Liu, J., Lv, H., Li, J., Wang, J., Deng, Y.J., Ran, L.H., Shi, X.L., Wang, X.Y., Wu, Q.F., Li, C.F., Ren, X.Y., Wang, J.Q., Wang, X.L., Li, D.W., Liu, D.Y., Zhang, X.W., Ji, Z.D., Zhao, W.M., Sun, Y.Q., Zhang, Z.P., Bao, J.Y., Han, Y.J., Dong, L.L., Ji, J., Chen, P., Wu, S.M., Liu, J.S., Xiao, Y., Bu, D.B., Tan, J.L., Yang, L., Ye, C., Zhang, J.F., Xu, J.Y., Zhou, Y., Yu, Y.P., Zhang, B., Zhuang, S.L., Wei, H.B., Liu, B., Lei, M., Yu, H., Li, Y.Z., Xu, H., Wei, S.L., He, X.M., Fang, L.J., Zhang, Z.J., Zhang, Y.Z., Huang, X.G., Su, Z.X., Tong, W., Li, J.H., Tong, Z.Z., Li, S.L., Ye, J., Wang, L.S., Fang, L., Lei, T.T., Chen, C., Chen, H., Xu, Z., Li, H.H., Huang, H.Y., Zhang, F., Xu, H.Y., Li, N., Zhao, C.F., Li, S.T., Dong, L.J., Huang, Y.Q., Li, L., Xi, Y., Qi, Q.H., Li, W.J., Zhang, B., Hu, W., Zhang, Y.L., Tian, X.J., Jiao, Y.Z., Liang, X.H., Jin, J., Gao, L., Zheng, W.M., Hao, B.L., Liu, S.Q., Wang, W., Yuan, L.P., Cao, M.L., McDermott, J., Samudrala, R., Wang, J., Wong, G.K., Yang, H. (2005). The genomes of Oryza sativa: A history of duplications. PLoS Biol. 3(2): 266-281.
30 Dohm, J.C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36(16): e105.
31 Van Os, H., Andrzejewski, S., Bakker, E., Barrena, I., Bryan, G.J., Caromel, B., Ghareeb, B., Isidore, E., de Jong, W., van Koert, P., Lefebvre, V. Milbourne, D. Ritter, E. van der Voort, J.N-A-M.R. Rousselle-Bourgeois, F. van Vliet, J. Waugh, R. Visser, R.G-F. Bakker, J. van Eck, H.J. (2006). Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated geneisolation and a genomewide physical map. Genetics. 173: 1075-1087.
32 Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G.S., et al. (2002). Green revolution: A mutant gibberellin-synthesis gene in rice. Nature. 416: 701-702.
33 Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H., and Turner, D.J. (2008). A large genome center’s improvements to the Illumina sequencing system. Nat. Methods. 5(12): 1005-1010.
34 Bennetzen, J.L. (2007). Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10: 176-181.
35 Tang, H.B., Bowers, J.E., Wang, X.Y., Ming, R., Alam, M., and Paterson, A.H. (2008). Synteny and collinearity in plant genomes. Science. 320: 486-488.
36 Sasaki, T., and Burr, B. (2000). International rice genome sequencing project: the effort to completely sequence the rice genome. Curr. Opin. Plant Biol. 3: 138-141.
37 Yu, J., et al. A draft sequence of the rrice genome (Oryza sativa L. ssp. indica). (2002). Science. 296: 79-92.
38 Feng, Q., Zhang, Y.J., Hao, P., Wang, S.Y., Fu, G., Huang, Y.C., Li, Y., Zhu, J.J., Liu, Y.L., Hu, X., Jia, P.X., Zhang, Y., Zhao, Q., Ying, K., Yu, S.L., Tang, Y.S., Weng, Q.J., Zhang, L., Lu, Y., Mu, J., Ku, Y.Q., Zhang, L-S., Yu, Z., Fan, D.L., Liu, X.H., Lu, T.T., Li, C., Wu, Y.R., Sun, T.G., Lei, H.Y., Li, T., Hu, H., Guan, J.P., Wu, M., Zhang, R.Q., Zhou, B., Chen, Z.H., Chen, L., Jin, Z.Q., Wang, R., Yin, H.F., Cai, Z., Ren, S.X., Lv, G., Gu, W.Y., Zhu, G.F., Tu, Y.F., Jia, J., Zhang, Y., Chen, J., Kang, H., Chen, X.Y., Shao, C.Y., Sun, Y., Hu, Q.P., Zhang, X.L., Zhang, W., Wang, L.J., Ding, C.W., Sheng, H.H., Gu, J.L., Chen, S.T., Ni, L., Zhu, F.H., Chen, W., Lan, L.F., Lai, Y., Cheng, Z.K., Gu, M.H., Jiang, J.M., Li, J.Y., Hong, G.F., Xue, Y.B., and Han, B. (2002). Sequence and analysis of rice chromosome 4. Nature. 420: 316-320.
39 International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature. 436: 793-800.
40 Ammiraju, J-S.S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A.C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C.Z., Goicoechea, J.T., Zuccolo, A., Chen, J.F., Bennetzen, J.L., Chen, M.S., Jackson, S.A., and Wing, R.A. (2008). Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell. 20: 3191-3209.
41 Vaughan, D.A. (1994). Wild relatives of rice: genetic resources handbook. (International Rice Research Institute, Manila, Philippines).
42 Aggarwal, R.K., Brar, D.S., and Khush, G.S. (1997). Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol. Gen. Genet. 254: 1-12.
43 Khush, G.S. (1997). Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35: 25-34.
44 Ge, S., Sang, T., Lu, B.R., and Hong, D.Y. (1999). Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA. 96: 14400-14405.
45 Ammiraju, J-S.S., Luo, M.Z., Goicoechea, J.L., Wang, W.M., Kudrna, D., et al. (2006). The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Research. 16:140-147.
46 Wing, R.A., Ammiraju, J-S.S., Luo, M.Z., Kim, H., Yu, Y., Kudrna, D., Goicoechea, J.L., Wang, W.M., Nelson, W., Rao, K., Brar, D., Mackill, D.J., Han, B., Soderlund, C., Stein, L., SanMiguel, P., and Jackson, S.A. (2005). The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. 59: 53-62.
47 FRARY, A., DOúANLAR, S. (2003). Comparative genetics of crop plant domestication and evolution. Turk. J. Agric. For. 27: 59-69.
48 Morishima, H. (2001). Evolution and domestication of rice. In Rice Genetics IV. Proc.of 4th Intern. Rice Genet. Symp. Edited by Khush, G.S., Brar, D.S., Hardy, B. New Delhi: Science Publishers, Inc: 63-77.
49 Tian, C.G., Xiong, Y.Q., Liu, T.Y., Sun, S.H., Chen, L.B., and Chen, M.S. (2005). Evidence for an ancient whole-genome duplication event in rice and other cereals. Acta Genetica Sinica. 32(5): 519-527.
50 Zou, X.H., Zhang, F.M., Zhang, J.G., Zang, L.L., Tang, L., Wang, J., Sang, T., and Ge, S. (2008). Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol. 9: R49.1-13.
51 Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J.C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.T., Stein, L., Ware, D., Jackson, S.A., Soderlund, C., and Wing, R.A. (2008). Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol. 9: R45.1-15.
52 Arumuganathan, K., and Earle, E.D. (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9(3): 208-218.
53 Piegu, B., Guyot, R., Picault, N., Roulin, A., Saniyal, A., Kim, H., Collura, K., Brar, D.S., Jackson, S.A., Wing, R.A., and Panaud, O. (2006). Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16: 1262-1269.
54 Ammiraju, J-S.S., Zuccolo, A., Yu, Y., Song, X., Piegu, B., Chevalier, F., Walling, J.G., Ma, J.X., Talag, J., Brar, D.S., SanMiguel, P., Jiang, N., Jackson, S.A., Panaud, O., and Wing, R.A. (2007). Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52: 342-351.
55 Kim, H., SanMiguel, P., Nelson, W., Collura, K., Wissotski, M., Walling, J.G., Kim, J.P., Jackson, S.A., Soderlund, C., and Wing, R.A. (2007). Comparative physical mapping between O. sativa (AA genome type) and O. punctata (BB genome type).Genetics. 176: 379-390.
56 Ma, J.X., Wing, R.A., Bennetzen, J.L., and Jackson, S.A. (2007). Evolutionary history and positional shift of a rice centromere. Genetics. 177: 1217-1220.
57 Zhang, S.B., Gu, Y.Q., Singh, J., Coleman-Derr, D., Brar, D.S., Jiang, N., and Lemaux, P.G. (2007). New insights into Oryza genome evolution: High gene colinearity and differential retrotransposon amplification. Plant Mol. Biol. 64: 589-600.
58 Lu, F., Ammiraju, J-S.S., Sanyal, A., Zhang, S.L., Song, R.T., Chen, J.F., Li, G.S., Sui, Y., Song, X., Cheng, Z.K., de Oliveira, A.C., Bennetzen, J.L., Jackson, S.A., Wing, R.A., and Chen, M.S. (2009). Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc. Natl. Acad. Sci. USA. 106: 2071-2076.
59 Mao L., Wood T.C., Yu Y., Budiman M.A., Tomkins J., Woo S-S., Sasinowski M., Presting G., Frisch D., Goff S., Dean R.A., and Wing, R.A. (2000). Rice transposable elements: A survey of 73,000 Sequence-Tagged-Connectors. Genome Res. 10: 982-990.
60 Bruggmann, R., Bharti, A.K., Gundlach, H., Lai, J.S., Young, S., Pontaroli, A.C., Wei, F.S., Haberer, G., Fuks, G., Du, C.G., Raymond, C., Estep, M.C., Liu, R.Y., Bennetzen, J.L., Chan, A.P., Rabinowicz, P.D., Quackenbush, J., Barbazuk, W.B., Wing, R.A., Birren, B., Nusbaum, C., Rounsley, S., Mayer, K.F-X., and Messing, J. (2006). Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16: 1241-1251.
61 Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A.K., and Khurana, J.P. (2007). F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol. 143: 1467-1483.
62 Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A.,Pachter, L.S., and Dubchak, I. (2000). VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 16: 1046-1047.
63 Huang, X.H., Lu, G.J., Zhao, Q., Liu, X.H., and Han, B. (2008). Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 148: 25-40.
64 Gaut, B.S., Morton, B.R., McCaig, B.C., Clegg, M.T. (1996). Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA. 93: 10274-10279.
65 Yang, Z.H., and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.
66 Zhang, Z., Li, J., Zhao, X.Q., Wang, J., Wong, G.K-S., and Yu, J. (2006). KaKs Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 4: 259-263.
67 Heinrichs, E.A., Medrano, F.G., and Rapusas, H.R. (1985). Genetic evaluation for insect resistance in rice. IRRI.
68 Jena, K.K., Khush, G.S. (1989). Monosomic alien addition lines of rice: production, morphology, cytology and breeding behavior. Genome. 32: 449-455.
69 Jena, K.K., Khush, G.S. (1990). Introgressron of genes from Oryza officinalis Well ex Watt to cultivated rice, O.saliva L. Theor. Appl. Genet. 80: 737-745.
70章琦,王春莲,施爱农等. (1994).野生稻抗稻白叶枯病性(Xanthomonas oryzae pv. oryzae)的评价.中国农业科学. 27: 1-9.
71颜辉煌,程祝宽,刘国庆,陈纯贤,闵绍楷,朱立煌. (1999).栽培稻——药用野生稻杂种F1及回交后代的基因组原位杂交鉴定.遗传学报. 26 (2): 157-162.
72卢宝荣. (1998).稻种遗传资源多样性的开发利用及保护.生物多样性. 6: 63-72.
73 Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
74 Hass, B.L., Pires, J.C., Porter, R., Phillips, R.L., Jackson, S.A. (2003). Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theor. Appl. Genet. 107: 773-782.
75 Zhang, W.L., Yi, C.D., Bao, W.D., Liu, B., Cui, J.J., Yu, H.X., Cao, X.F., Gu, M.H., Liu, M., Cheng, Z.K. (2005). The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol. 139: 306-315.