Population structure in Japanese rice population

Breeding Science

Volumn 63, Issue 1, 2013, Pages 49-57

  Yamasaki, Masanori ^a   Ideta, Osamu ^b,c  

^a KOBE UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^c NATIONAL AGRICULTURAL RESEARCH CENTER FOR WESTERN REGION   (Japan)

Author keywords

Genetic diversity; Japanese rice cultivars; Japanese rice diverse cultivars; Pedigree; Population structure; Simple sequence repeat

Indexed keywords

ORYZA SATIVA (JAPONICA CULTIVAR-GROUP);

EID: 84876944761     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.63.49     Document Type: Review

References (37)

1. Akagi, H., Y. Yokozeki, A. Inagaki and T. Fujimura (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet. 94: 61-67.
2. Brown, A.H.D. (1989) The case for core collection. In: Brown, A.H.D., O.H. Frankel, D.R. Marshall and J.T. Williams (eds.) The Use of Plant Genetic Resources, Cambridge University Press, Cambridge, pp. 136-156.
3. Buckler, E.S., J.B. Holland, P.J. Bradbury, C.B. Acharya, P.J. Brown, C. Browne, E. Ersoz, S. Flint-Garcia, A. Garcia, J.C. Glaubitz et al. (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
4. Doebley, J.F., B.S. Gaut and B.D. Smith (2006) The molecular genetics of crop domestication. Cell 127: 1309-1321.
5. Ebana, K., Y. Kojima, S. Fukuoka, T. Nagamine and M. Kawase (2008) Development of mini core collection of Japanese rice landrace. Breed. Sci. 58: 281-291.
6. Excoffier, L.G., P.E. Smouse and J.M. Quattro (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
7. Excoffier, L.G., G. Laval and S. Schneider (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinfom. Online 1: 47-50.
8. Falush, D., M. Stephens and J.K. Pritchard (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
9. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
10. Frankel, O.H. (1984) Genetic perspectives of germplasm conservation. In: Arber, W.K., K. Llimensee, W.J. Peacock and P. Stralinger (eds.) Genetic Manipulation: Impact on Man and Society, Cambridge University Press, Cambridge, pp. 161-170.
11. Garris, A.J., T.H. Tai, J. Coburn, S. Kresovich and S. McCouch (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638.
12. Goudet, J. (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. J. Heredity 86: 485-486.
13. Hashimoto, Z., N. Mori, M. Kawamura, T. Ishii, S. Yoshida, M. Ikegami, S. Takumi and C. Nakamura (2004) Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers. Theor. Appl. Genet. 109: 1586- 1596.
14. Ideta, O., I. Kono, Y. Takeuchi, H. Hirabayashi, M. Hirayama, H. Ohta, H. Sato, I. Ando, H. Kato, H. Nemoto et al. (2012) Diversity and relationships between coefficient of parentage and genetic distance estimated by SSR markers in Japanese rice cultivars. Breed. Res. 14: 106-113.
15. Imbe, T. (2002) Rice breeding in Japan. Res. J. Food and Agric. 25: 35-41.
16. Kojima, Y., K. Ebana, S. Fukuoka, T. Nagamine and M. Kawase (2005) Development of an RFLP-based rice diversity research set of germplasm. Breed. Sci. 55: 431-440.
17. Kushibuchi, K. (1997) In: Science of the Rice Plant Volume 3 Genetics, Matsuo, T., Y. Futsuhara, F. Kikuchi and H. Yamagata (eds.) Nobunkyo, Tokyo.
18. Langella, O. (2007) Populations 1.2.30: Population genetic software (individuals or populations distances, phylogenetic trees). http://bioinformatics.org/~tryphon/populations/
19. Liu, K., M. Goodman, L. Muse, J.S. Smith, E. Buckler and J. Doebley (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117-2128.
20. Liu, K. and S.V. Muse (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128- 2129.
21. McMullen, M.D., S. Kresovich, H. Sanchez Villeda, P. Bradbury, H. Li, Q. Sun, S. Flint-Garcia, J. Thornsberry, C. Acharya, C. Bottoms et al. (2009) Genetic properties of the maize nested association mapping population. Science 325: 737-740.
22. Monna, L., R. Ohta, H. Masuda, A. Koike and Y. Minobe (2006) Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.). DNA Res. 13: 43-51.
23. Nagasaki, H., K. Ebana, T. Shibaya, J. Yonemaru and M. Yano (2010) Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population. Breed. Sci. 60: 648-655.
24. Peakall, R. and P.E. Smouse (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Eco. Notes 6: 288-295.
25. Pritchard, J.K., M. Stephens and P. Donnelly (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945- 959.
26. Saisho, D. and M.D. Purugganan (2007) Molecular phylogeography of domesticated barley traces expansion of agriculture in the old world. Genetics 177: 1765-1776.
27. Sakai, K.I. (1957) Theoretical studies on plant breeding technique. V. Coefficient relationship in the breeding of autogamous plants. Jpn. J. Breed. 7: 87-92.
28. Sugiura, N., T. Tsuji, K. Fujii, T. Kato, N. Saka, T. Touyama, Y. Hayano-Saito and T. Izawa (2004) Molecular marker-assisted selection in a recurrent backcross breeding for the incorporation of resistance to rice stripe virus and panicle blast in rice (Oryza sativa L.). Breed. Res. 6: 143-148.
29. Tabuchi, H., Y.I. Sato and I. Ashikawa (2007) Mosaic structure of Japanese rice genome composed mainly of two distinct genotypes. Breed. Sci. 57: 213-221.
30. Vaughan, D.A. (1991) Choosing rice germplasm for evaluation. Euphytica 54: 147-154.
31. Wright, S. (1922) Coefficients of inbreeding and relationship. Amer. Nat. 56: 330-338.
32. Wright, S.I., I. Vroh Bi, S.G. Schroeder, M. Yamasaki, J.F. Doebley, M.D. McMullen and B.S. Gaut (2005) The effect of artificial selection on the maize genome. Science 308: 1310-1314.
33. Yamamoto, T., H. Nagasaki, J. Yonemaru, K. Ebana, M. Nakajima, T. Shibaya and M. Yano (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genetics 11: 267.
34. Yamasaki, M., M.I. Tenaillon, I. Vroh Bi, S.G. Schroeder, H. Sanchez-Villeda, J.F. Doebley, B.S. Gaut and M.D. McMullen (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17: 2859-2872.
35. Yan, J., T. Shah, M.L. Warburton, E.S. Buckler, M.D. McMullen and J. Crouch (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One 4(12): e8451.
36. Yu, J., J.B. Holland, M.D. McMullen and E.S. Buckler (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
37. Zhang, D., H. Zhang, M. Wang, J. Sun, Y. Qi, F. Wang, X. Wei, L. Han, X. Wang and Z. Li (2009) Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor. Appl. Genet. 119: 1105-1117.