Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.)

Xiangqian Zhao; Long Yang; Yan Zheng; Zhaohua Xu; Weiren Wu

doi:10.1016/S1673-8527(08)60133-2

Volume 36 Issue 7

Jul. 2009

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2009 > 36(7): 435-442

PDF( 262 KB)

Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.)

doi: 10.1016/S1673-8527(08)60133-2

a
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
b
College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China

More Information

Corresponding author: E-mail address: wuwr@zju.edu.cn (Weiren Wu)
Received Date: 2008-11-02
Accepted Date: 2009-03-17
Rev Recd Date: 2009-03-01

Available Online: 2009-07-23

Publish Date: 2009-07-20

Abstract

Abstract

It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice (O. sativa). However, how the two subspecies of O. sativa (indica and japonica) were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism (SSILP) markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups: one group (Group I) comprises all the O. rufipogon accesions from tropical (South and Southeast) Asia as well as the standard indica rice; the other group (Group II) comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. rufipogon might occur after its speciation from other AA-genome species.
- evolution,
- SSILP marker

FullText(HTML)

References(36)

References

[1]	Bautista, N.S., Solis, R., Kamijima, O. et al. RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice Genes Genet. Syst., 76 (2001),pp. 71-79
[2]	Becker, J., Heun, M. Barley microsatellites: Allele variation and mapping Plant Mol. Biol., 27 (1995),pp. 835-845
[3]	Chang, T.T. The origin, evolution, clutivation, dissemination and diversification of Asian and African rice Euphytica, 25 (1976),pp. 323-334
[4]	Cheng, C.Y., Motohashi, R., Tsuchimoto, S. et al. Polyphyletic origin of cultivated rice: Based on the interspersion pattern of SINEs Mol. Biol. Evol., 20 (2003),pp. 67-75
[5]	Dally, A.M., Second, G. Theor. Appl. Genet., 80 (1990),pp. 209-222
[6]	Hampl, V., Pavlicek, A., Flegr, J. Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: Application to trichomonad parasites Int. J. Syst. Evol. Microbio., 51 (2001),pp. 731-735
[7]	Hirano, H.Y., Mochizuki, K., Umeda, M. et al. J. Mol. Evol., 38 (1994),pp. 132-137
[8]	Ishii, T., Xu, Y.B., McCouch, S.R. Nuclear- and chloroplast-microsatellite variation in A-genome species of rice Genome, 44 (2001),pp. 658-666
[9]	Khush, G.S. Origin, dispersal, cultivation and variation of rice Plant Mol. Biol., 35 (1997),pp. 25-34
[10]	Li, C.B., Zhou, A.L., Sang, T. Rice domestication by reducing shattering Science, 311 (2006),pp. 1936-1939
[11]	Lin, H.N., Zhu, W., Silva, J.C. et al. Intron gain and loss in segmentally duplicated genes in rice Genome Biol., 7 (2006),p. R41
[12]	Londo, J.P., Chiang, Y.C., Hung, K.H. et al. Proc. Natl. Acad. Sci. USA, 103 (2006),pp. 9578-9583
[13]	Lu, B.R., Zheng, K.L., Qian, H.R. et al. Genetic differentiation of wild relatives of rice as assessed by RFLP analysis Theor. Appl. Genet., 106 (2002),pp. 101-106
[14]	Ma, J.X., Bennetzen, J.L. Rapid recent growth and divergence of rice nuclear genomes Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 12404-12410
[15]	Mochizuki, K., Ohtsubo, H., Hirano, H. et al. Classification and relationships of rice strains with AA genome by identification of transposable elements at nine loci Jpn. J. Genet., 68 (1993),pp. 205-217
[16]	Morishima, H.
[17]	Murray, M.G., Thompson, W.E. Rapid isolation of highmolecular-weight plant DNA Nucleic Acids. Res., 8 (1980),pp. 4321-4325
[18]	Nei, M. Estimation of average heterozygosity and genetic distance from a small number of individuals Genetics, 89 (1978),pp. 583-590
[19]	Oka, H.I. Experimental studies on the origin of cultivated rice Genetics, 78 (1974),pp. 475-486
[20]	Oka, H.I.
[21]	Oka, H.I., Morishima, H. Evolution, 21 (1967),pp. 249-258
[22]	Oka, H.I., Morishima, H. Euphytica, 31 (1982),pp. 41-50
[23]	Rakshit, S., Rakshit, A., Matsumura, H. et al. Theor. Appl. Genet., 114 (2007),pp. 731-743
[24]	Rogozin, I.B., Wolf, Y.I., Sorokin, A.V. et al. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution Curr. Biol., 13 (2003),pp. 1512-1517
[25]	Rose, A.B.
[26]	Roy, S.W., Gilbert, W. Rates of intron loss and gain: Implications for early eukaryotic evolution Proc. Natl. Acad. Sci. USA, 102 (2005),pp. 5773-5778
[27]	Second, G. Jpn. J. Genet., 57 (1982),pp. 25-57
[28]	Tang, T., Lu, J., Huang, J. et al. Genomic variation in rice: Genesis of highly polymorphic linkage blocks during domestication PLoS Genet., 2 (2006),p. e199
[29]	Ting, Y. The origin and evolution of cultivated rice in China Scientia Agricultura Sinica, 8 (1957),pp. 242-260
[30]	Vaughan, D.A., Morishima, H., Kadowaki, K. Curr. Opin. Plant Biol., 6 (2003),pp. 139-146
[31]	Wang, X.K., Sun, C.Q.
[32]	Wang, X.S., Zhao, X.Q., Zhu, J. et al. DNA Res., 12 (2005),pp. 417-427
[33]	Wang, Z.Y., Second, G., Tanksley, S.D. Theor. Appl. Genet., 83 (1992),pp. 565-581
[34]	Williams, J.G.K., Kubelik, A.R., Livak, K.J. et al. DNA polymorphism amplified by arbitrary primers are useful as genetic markers Nucleic Acids. Res., 18 (1990),pp. 6531-6535
[35]	Yang, L., Jin, G.L., Zhao, X.Q. et al. PIP: A database of potential intron polymorphism markers Bioinformatics, 23 (2007),pp. 2174-2177
[36]	Zietkiewicz, E. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerize chain reaction amplification Genomics, 20 (1994),pp. 176-183