Genomic and species divergences in rice offer a major advantage in genetic and evolutional studies, as well as for practical breeding purposes. The genus Oryza is classified into nine genomes comprising 23 species (two cultivated and 21 wild). Classification of the genome has been made based on the ability of a known tester genome to form paired bivalent chromosomes during meiosis in an F1 hybrid with an accession of unknown genome. Varied levels of partial sterility have been observed in the crosses between a variety of accessions, both across species as well as within a species, suggesting continuous evolution of the genome. The pattern of genome and chromosomal evolution of the genus Oryza and of the family Poaceae has been resolved progressively over the last decades. The observed results, possible relationships and impact on genome and chromosome evolution are reviewed in this chapter.
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References
Aggarwal RK, Brar DS, Khush GS (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.
Ammiraju JSS, Luo M, Goicoechea JL, 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 Res 16:140–147.
Bao W, Zhang W, Yang Q, Zhang Y, Han B, Gu M (2006) Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis. Mol Gen Genet 275:421–430.
Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J (2001) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749–1757.
Cheng Z, Dong F, Langdon T, et al. (2002) Functional centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704.
Devos KM (2005) Updating the ‘crop circle’. Curr Opinion Plant Biol 8:155–162.
Devos KM, Gale, MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35:3–15.
Fukui K, Shishido R, Kinoshita T (1997) Identification of the rice D-genome chromosomes by genomic in situ hybridization. Theor Appl Genet 95:1239–1245.
Guo X, Xu G, Zhang Y, Wen X, Hu W, Fan L (2006) Incongruent evolution of chromosomal size in rice. Genet Mol Res 30:373–389.
Hass-Jacobus B, Futrell-Griggs M, Abernathy B, et al. (2006) Integration of hybridization-based markers (overgoes) into physical maps for comparative and evolutionary explorations in the genus Oryza and in sorghum. BMC Genomics 7:199–214.
Hu CH (1961) Comparative karyological studies of wild and cultivated species of Oryza. Taiwan Provincial College of Agriculture, Taichung.
Ilic K, SanMigiuel PJ, Bennetzen JL (2003) A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100:12265–12270.
Katayama T (1990) Relationships between chromosome numbers and genomic constitutions in genus Oryza. In: Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H (eds) Science of the rice plant, vol 3, Genetics, pp 39–48. Food and Agriculture Policy Research Center Press, Tokyo.
Khush GS (1990) Report of meetings to discuss chromosome numbering system in rice. Rice Genet Newslett 7:12–15.
Khush GS, Singh RJ, Sur SC, Librojo AL (1984) Primary trisomics of rice. Origin, morphology, cytology and use in linkage mapping. Genetics 107:141–163.
Kurata N (1985) Chromosome analysis of meiosis and mitosis in rice. Rice Genetics I:143–152. International Rice Research Institute, Manila.
Kurata N, Fukui K (2003) Chromosome research in genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza, pp 213–261. Science Publishers, Enfield, USA, Plymouth UK.
Kurata N, Omura T (1978) Karyotype analysis in rice. I. A new method for identifying all chromosome pairs. Jpn J Genet 53:251–255.
Kurata N, Nonomura K, Harushima Y (2002) Rice genome organization: the centromere and genome interactions. Annals Botany 90:427–435.
Lee H-R, Zhang W, Langdon T, et al. (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci USA 102:11793–11798.
Lin H, Zhu W, Silva JC, Gu X, Buell CR (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 7:R41.
Lu J, Tang H, Huang J, Shi S, Wu C-I (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet 22:126–131.
Ma J, Bennetzen JL (2006) Recombination, rearrangement, reshuffling and divergence in a centromeric region of rice. Proc Natl Acad Sci USA 103:383–388.
Miyabayashi T, Nonomura K-I, Kurata N (2007) Genome size determination of twenty wild Oryza species by flow cytometric and chromosome analyses. Breed Sci 57:73–78.
Moore G, Aragon-Alcaide L, Roberts M, Reader S, Miller T, Foote T (1997) Are rice chromosomes components of a holocetric chromosome ancestor? Plant Mol Biol 35:17–23.
Nandi HK (1936) The chromosome morphology, secondary association and origin of cultivated rice. J Genet 33:315–336.
Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903–9908.
Piegu B, Guyot R, Picault N, et al. (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.
Sakai K (1935) Study of rice chromosomes. 1. Secondary pairing of meiotic chromosomes. Jpn J Genet 11:145–156 (in Japanese).
Sasaki T, Matsumoto T, Antonio BA, Nagamura Y (2005) From mapping to sequencing, post-sequencing and beyond. Plant Cell Physiol 46:3–13.
Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35:791–799.
Wing R, Ammiraju JSS, Luo M, et al. (2005) The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62.
Wing R, Luo M, Goicoechea JL, et al. (2006a) 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 Res 16:140–147.
Wing R, Kim HR, Goicoechea JL, et al. (2006b) The Oryza map aligment project: a new resource for comparative genomic studies within Oryza. Proc 4th Int Rice Funct Genomics Symp 11.
Wu J, Kurata N, Tanoue H, et al. (1998) Physical mapping of duplicated genomic regions of two chromosome ends in rice. Genetics 150:1595–1603.
Yu J, Wang J, Lin W, et al. (2005) The genomes of Oryza sativa: a history of duplication. Plos Biol 3:266–281.
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Kurata, N. (2008). Chromosome and Genome Evolution in Rice. In: Hirano, HY., Sano, Y., Hirai, A., Sasaki, T. (eds) Rice Biology in the Genomics Era. Biotechnology in Agriculture and Forestry, vol 62. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74250-0_18
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