Abstract
In order to estimate genetic diversity of rice (Oryza sativa L.) germplasm in Yunnan Province of China, 60 varieties from different regions were analyzed by microsatellite (SSR) fingerprints. Nine selected SSR primer pairs amplified a total of 55 alleles from these varieties, and high genetic diversity (0.706) was found, although it was not evenly distributed across the regions. Marked genetic variation was detected within the traditional varieties. A UPGMA dendrogram based on SSR polymorphism indicated a great variation among the rice varieties, with coefficients ranging between 0.229 and 1.000. The formation of the rice diversity pattern in Yunnan is associated with natural conditions and especially with diverse cultural demands and farming styles. Strategic conservation of rice germplasm in Yunnan is important, and this could be implemented by collecting varieties across geographic regions with sufficient individuals within the same varieties. Effective rice conservation should also consider cultural aspects during collection.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Akagi H, Yokezeki Y, Inagaki A, Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeat, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94:61–67
Chang TT (1976) The origin, evolution, cultivation, dissemination, and diversification of Asian and African rice. Euphytica 25:425–441
Chen ZZ, Wang XS, Zhu J (2005) Analysis of SSR polymorphism by genome scale comparing between varieties in rice. Chin Rice Sci 19(4):303–307
Garris A, Tai T, Coburn J, Kresovich S, McCouch SR (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638
Guo XP, Zhao YM (1998) SSR technique and its application in plant genetics and breeding. Acta Agr Boreali Sin 13:73–76 (in Chinese with English abstract)
He FH, Zeng RZ, Xi ZY, Talukdar A, Zhang GQ (2003) Genetic diversity of different waxy genotypes in rice. Mol Plant Breed 1(2):179–186
Ishii T, Xu Y, McCouch SR (2001) Nuclear and chloroplast microsatellite in A-genome species of rice. Genom 44:658–666
Junjian N, Peter MC, David JM (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42:601–607
Kimura M, Crow JF (1964) The number of alleles that can be maintained. Genetics 49:725–738
Lewontin RC (1972) The apportionment of human diversity. In: Dobzhansky T (ed) Evolutionary biology, vol VI. Appleton-Century-Crofts, New York, pp 381–398
Lu B-R, Snow AA (2005) Gene flow from genetically modified rice and its environmental consequences. BioScience 55:669–678
Lu B-R, Zhu YY, Wang YY (2002a) The current status and perspectives of on-farm conservation of crop genetic diversity. Biodiv Sci 10(4):409–415
Lu B-R, Zheng KL, Qian HR, Zhuang JY (2002b) Genetic differentiation of wild relatives of rice as referred by the RFLP analysis. Theor Appl Genet 106:101–106
McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207
Normile D (1997) Archaeology: Yangtze seen as earliest rice site. Science 275:309
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Oka HI (1988) Origin of cultivated rice. Development in crop species. Japan Scientific Societies Press, Tokyo
Rohlf FJ (1994) NTSYS-pc, Numerical Taxonomy and Multivariate Analysis System, Ver. 1. 80. Exeter Software, New York
Song ZP, XU X, Wang B, Chen JK, Lu BR (2003) Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers. Theor Appl Genet 107:1492–1499
Watterson GA (1974) The sampling theory of selectively neutral alleles. Adv Appl Prob 6:463–488
Yeh FC, Yang RC, Boyle T (1999) Microsoft Window-based Freeware for Population Genetic Analysis (PopGene), Ver. 1.31. ftp://ftp.microsoft. -com/softlib/mslfiles/hpgl.exe
Ying CS (2000) Conservation and utilization of rice genetic resource in China. China Rice Res Newsl 8:13–14 (in Chinese with English abstract)
Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aquino C, Virmani SS, Li ZK (2003) Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor Appl Genet 108:131–140
Zeng LJ, Zheng CM (2001) SSR technique and its application. China Trop Agr 91:56–59 (in Chinese)
Zhang H, Shen S, Wang X, Zeng Y, Li Z, Yang Z (2001) Ecological and genetic diversity of rice germplasm in Yunnan, China. PGR Newsl 125:24–28
Zhu MY, Wang YY, Zhu YY, Lu BR (2004) Estimating genetic diversity of rice landraces from Yunnan by SSR assay and its implication for conservation. Acta Bot Sin 46:1458–1467
Zhu YY, Wang YY, Chen HR, Lu BR (2003) Conserving traditional rice through biodiversity management. BioScience 53:158–162
Acknowledgments
This research is supported by the National Fundamental Research Program (Grant no. 2006CB100205) and the Italian Ministry of Environment and Environmental Protection, within the research project “Application of biotechnology to the protection of the environment in collaboration with China (years 2005–2007).”
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Tu, M., Lu, BR., Zhu, Y. et al. Abundant Within-varietal Genetic Diversity in Rice Germplasm from Yunnan Province of China Revealed by SSR Fingerprints. Biochem Genet 45, 789–801 (2007). https://doi.org/10.1007/s10528-007-9118-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10528-007-9118-6