Korean Journal of Breeding Science (한국육종학회지)

The Korean Society of Breeding Science (한국육종학회)
권호 표지

SSR Diversity in Japonica Rice Cultivars and its Association to Several Traits

자포니카 벼 품종의 SSR 다양성과 몇 가지 농업형질과의 연관

Gwon, Su-Jin;An, Sang-Nak;Hong, Ha-Cheol;Hwang, Hong-Gu;Choe, Hae-Chun
권수진;안상낙;홍하철;황홍구;최해춘

  • Published : 20020000
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Abstract

Diversity of 80 japonica rice cultivars was evaluated using 65 microsatellite or simple sequence repeat (SSRs) markers. Sixty-five microsatellite markers representing 65 loci in the rice genome detected polymorphisms among the 80 cultivars and revealed 289 alleles with a mean of 4.45 alleles per primer. The polymorphism information content (PIC) value ranged from 0.02 to 0.86, with an average of 0.43. The 80 cultivars were classified into nine groups by cluster analysis based on Nei`s genetic distances. Also, the 80 cultivars were evaluated for five traits of agronomic importance including panicle number. One-way analysis of variance was carried out to find out significant relationships between individual markers and phenotypes. Eight, five and three markers showed an association with panicle length, spikelets per panicle and 1,000 grain weight, respectively and this result needs to be confirmed using a segregating population for these traits. This preliminary work provides the basis for a large scale evaluation of molecular diversity of germplasm.

Keywords

References

  1. Anderson JA, Churchill GA, Autrigue JE, Tanksley SD 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181-186 https://doi.org/10.1139/g93-024
  2. Akagi H, Yokozeki Y, Inagaki A, Fujimura T 1996. Microsatellite DNA markers for rice chromosome. Theor. Appl. Genet. 93:1071-1077 https://doi.org/10.1007/BF00230127
  3. Akkaya MS, Shoemaker RC, Specht JE, Bhagwat AA, Cregan PB 1995. Integration of simple sequence repeat DNA markers into a soybean linkage map. Crop Sci. 35:1439-1445 https://doi.org/10.2135/cropsci1995.0011183X003500050030x
  4. Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu KS, Xiao JH, Yu ZH, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251-1274
  5. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Qryza sativa L.). Theor. Appl. Genet. 95:553-567 https://doi.org/10.1007/s001220050596
  6. Cho YG, McCouch SR, Kuiper M, Kang MR, Pot J, Groenen JTM, Eun MY 1998. Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.). Theor. Appl. Genet. 97:370-380 https://doi.org/10.1007/s001220050907
  7. Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE 1999. An integrated genetic linkage map of the soybean genome. Crop Sci. 39:1464-1490 https://doi.org/10.2135/cropsci1999.3951464x
  8. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Mirissette J, Weissenbach J 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature(London) 380:152-154 https://doi.org/10.1038/380152a0
  9. Dietrich WF, Miller J, Steen R, Merchant MA, DamronBoles D, Husain Z, Dredge R, Daly MJ, Ingalls KA, O'Connor TJ, Evans CA, DeAngelis MM, Levinson DM, Kruglyak L, Goodman N, Copelang NG, Jenkins NA, Hawkins TL, Stein L, Page DC, Lander ES 1996. A comprehensive genetic map of the mouse genome. Nature (London) 380:149-152 https://doi.org/10.1038/380149a0
  10. Ji HS, Koh HJ, Park SU, McCouch SR 1998. Varietal identification in Japonica rice using microsatellite DNA markers. Korean J. Breeding 30(4):350-360
  11. Kim KH, Cho SY, Moon HP, Choi HC 1994. Breeding strategy for improvement and diversification of grain quality in rice (in Korean). Korean J. Breeding 26 (Supp.2):3-19
  12. Kwon SJ, Ahn SN, Choi HC, Moon HP 1999. Evaluation of genetic relationship and fingerprinting of rice varieties using microsatellite and RAPD markers. Korean J. Crop Sci. 44(2):112-116
  13. Kwon SJ, Ahn SN, Suh JP, Cho YC, Hong HC, Kim YK, Hwang HG, Moon HP, Choi HC 2000a. Genetic mapping and identification of QTLs related to agronomic traits in a Japonica cross of rice. Proc. $1^{st}$ Symp. Plant Mol. Genet. Breeding, Poster 12. Seoul Nat'l Univ., Suwon, Korea (Sept. 1, 2000)
  14. Kwon SJ, Ahn SN, Suh JP, Hong HC, Kim YK, Hwang HG, Moon HP, Choi HC 2000b. Genetic diversity of Korean native rice varieties. Korean J. Breeding 32(2):186-193
  15. Mackill DJ, Zhang Z, Redona ED, Colowit PM 1996. Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969-977 https://doi.org/10.1139/g96-121
  16. National Academy of Sciences 1972. Genetic vulnerability of major crops. National Academy of Science, Washington, D.C
  17. Nei M, Li WH 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Nat'l. Acad. Sci. U.S.A. 76:5269-5273 https://doi.org/10.1073/pnas.76.10.5269
  18. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR 1997. Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40:370-378 https://doi.org/10.1139/g97-050
  19. Panaud O, Chen X, McCouch SR 1996. Development of microsatellite markers and charaterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol. Gen. Genet. 252:597-607
  20. Ramsay L, Macaulay M, degli Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R 2000. A simple sequence repeat-based linkage map of barley. Genetics 156:1997-2005
  21. Richards R, Sutherland GR 1994. Simple repeat DNA is not replicated simply. Nat. Genet. 6:114-116 https://doi.org/10.1038/ng0294-114
  22. Temnykh S, Cartinhour S, Park W, Ayres N, Hauck N, Lipovich L, Cho YG, McCouch SR 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:697-712 https://doi.org/10.1007/s001220051342
  23. Temnykh S, De Clerck G, Lukashova A, Lipovitch L, Cartinhour S, McCouch SR 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1452 https://doi.org/10.1101/gr.184001
  24. Wu KS, Tanksley SD 1993. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol. Gen. Genet. 241:225-235 https://doi.org/10.1007/BF00280220
  25. Xiao J, Li J, Grandillo S, Ahn S, Yuan L, Tanksley SD, McCouch SR 1998. Identification of trait-improving QTL alleles from a wild rice relative, Oryza rufipogon. Genetics. 150: 899-909
  26. Xiao J, Li J, Yuan L, Tanksley SD 1996. Identification of QTLs affecting traits of agronomic importance in recombinant inbred population derived from a subspecific rice cross. Theor. Appl. Genet. 92:230-244 https://doi.org/10.1007/BF00223380