Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites

doi:10.1016/S1671-2927(00)8710

Journal of Integrative Agriculture ›› 2012, Vol. 12 ›› Issue (11): 1755-1766.DOI: 10.1016/S1671-2927(00)8710

• 论文 • 下一篇

Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites

ZHANG Dong-ling, WANG Mei-xing, QI Yong-wen, SUNJun-li, WANG Feng-mei, LI Jin-jie, ZHANG Hong-liang, and LI Zi-chao

1.Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R.China
2.Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R.China
3.Guangzhou Sugarcane Industry Research Institute, Guangzhou 510316, P.R.China
4.Ministry of Agriculture, Beijing 100026, P.R.China

出版日期:2012-11-01 发布日期:2012-11-24
通讯作者: Correspondence ZHANG Hong-liang, Tel: +86-10-62734018, Fax: +86-10-62731414, E-mail: zhangl@cau.edu.cn; LI Zi-chao, Tel/Fax: +86-10-62731414, E-mail: lizichao@cau.edu.cn
基金资助:
This research was supported by the National Basic Research Program of China (2010CB125904, 2004CB117201) and the National Natural Science Foundation of China (30871506).

Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites

ZHANG Dong-ling, WANG Mei-xing, QI Yong-wen, SUNJun-li, WANG Feng-mei, LI Jin-jie, ZHANG Hong-liang, and LI Zi-chao

1.Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R.China
2.Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R.China
3.Guangzhou Sugarcane Industry Research Institute, Guangzhou 510316, P.R.China
4.Ministry of Agriculture, Beijing 100026, P.R.China

Online:2012-11-01 Published:2012-11-24
Contact: Correspondence ZHANG Hong-liang, Tel: +86-10-62734018, Fax: +86-10-62731414, E-mail: zhangl@cau.edu.cn; LI Zi-chao, Tel/Fax: +86-10-62731414, E-mail: lizichao@cau.edu.cn
Supported by:
This research was supported by the National Basic Research Program of China (2010CB125904, 2004CB117201) and the National Natural Science Foundation of China (30871506).

摘要/Abstract

摘要： China is one of the largest centers of genetic diversity of Oryza sativa L. and is the original centers of Oryza sativa L. subspecies japonica. Using a genetically representative core collection of 1 442 rice landraces of japonica in China, the genetic structure, differentiation, and geographic diversity were analyzed. The model-based structure analysis on varieties within three ecotypes revealed 16 eco-geographical types, which are partially accorded with some of the ecological zones in China. The differentiation of eco-geographical types contributed to the local ecological adaption and physical isolation, and maybe could be used to develop the heterotic groups of japonica. To facilitate the identification of different ecotypes and eco-geographical types, we provided the SSR character alleles of each ecotype or geographical eco-group and a rapid discriminated method based on these character alleles. Lastly, investigation on genetic diversity, genetic differentiation indicated that southwest region of China, including south of Yunnan Province, northwest of Guangxi Zhuang Autonomous Region, and southwest of Guizhou Province, possessed the highest genetic diversity and all the necessary conditions as a center of genetic diversity and should be the center of genetic diversity of rice landraces of japonica in China.

关键词: japonica rice, population structure, eco-geographical differentiation, China, microsatellites

Abstract: China is one of the largest centers of genetic diversity of Oryza sativa L. and is the original centers of Oryza sativa L. subspecies japonica. Using a genetically representative core collection of 1 442 rice landraces of japonica in China, the genetic structure, differentiation, and geographic diversity were analyzed. The model-based structure analysis on varieties within three ecotypes revealed 16 eco-geographical types, which are partially accorded with some of the ecological zones in China. The differentiation of eco-geographical types contributed to the local ecological adaption and physical isolation, and maybe could be used to develop the heterotic groups of japonica. To facilitate the identification of different ecotypes and eco-geographical types, we provided the SSR character alleles of each ecotype or geographical eco-group and a rapid discriminated method based on these character alleles. Lastly, investigation on genetic diversity, genetic differentiation indicated that southwest region of China, including south of Yunnan Province, northwest of Guangxi Zhuang Autonomous Region, and southwest of Guizhou Province, possessed the highest genetic diversity and all the necessary conditions as a center of genetic diversity and should be the center of genetic diversity of rice landraces of japonica in China.

Key words: japonica rice, population structure, eco-geographical differentiation, China, microsatellites

ZHANG Dong-ling, WANG Mei-xing, QI Yong-wen, SUNJun-li, WANG Feng-mei, LI Jin-jie, ZHANG Hong-liang, and LI Zi-chao. Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites[J]. Journal of Integrative Agriculture, 2012, 12(11): 1755-1766.

ZHANG Dong-ling, WANG Mei-xing, QI Yong-wen, SUNJun-li , WANG Feng-mei, LI Jin-jie, ZHANG Hong-liang, and LI Zi-chao. Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites[J]. Journal of Integrative Agriculture, 2012, 12(11): 1755-1766.

参考文献

[1]Anderson J A, Churchill G A, Autrique J E, Tanksley S D,Sorrells M E. 1993. Optimizing parental selection forgenetic linkage maps. Genome, 36, 181-186.

[2]Bassam B J, Caetano A G, Gresshoff P M. 1991. Fast andsensitive silver staining of DNA in polyacrylamide gels.Analytical Biochemistry, 196, 80-83.

[3]Cheng C Y, Motohashi R, Tsuchimoto S, Fukuta Y, OhtsuboH, Ohtsubo E. 2003. Polyphyletic origin of cultivatedrice: based on the interspersion pattern of SINEs.Molecular Biology and Evolution, 20, 67-75.

[4]Cheng K S, Zhou J W, Lu Y X, Luo J, Huang N W, Liu G R,Wang X K. 1984. Studies on the indigenous rices inYunnan and their utilization II. Revised classificationof Asian cultivated rice. Acta Agronomica Sinica, 10,271-280.

[5]Doi K, Sobrizal K, Ikeda K, Sanchez TK, Nagai Y, YoshimuraA. 2002. Developing and evaluating rice chromosomesegment substitution lines. In: IRRI ConferenceSeptember 16-19, 2002.

[6]International Rice ResearchInstitute, Beijing. pp. 275-287.

[7]Evanno G, Regnaut S, Goudet J. 2005. Detecting the numberof clusters of individuals using the software structure:a simulation study. Molecular Ecology, 14, 2611-2620.

[8]Falush D, Stephens M, Pritchard J K. 2003. Inference ofpopulation structure using multilocus genotype data:linked loci and correlated allele frequencies. Genetics,164, 1567-1587.

[9]Glaszmann J C. 1987. Isozymes and classification of Asianrice varieties. Theoretical and Applied Genetics, 74,21-30.

[10]Goudet J. 2001. FSTAT, a program to estimate and testgene diversities and fixation indices (ver. 2.9.3). [2005-6-23]. http://www.unil.ch/izea/softwares/fstat.htmlHurlbert S H. 1971. The nonconcept of species diversity: acritique and alternative parameters. Ecology, 52, 577-586.

[11]ICGR CAAS (Institute of Crop Germplasm Resources ofChina Academy of Agricutural Science). 1996. In:Catalogue of Rice Germplasm Resources in China(1988-1993). China Agricultural Press, Beijing.

[12]Kato S H K, Hara S. 1928. On the affinity of rice varieties asshown by the fertility of rice plants. CentralAgricultural Institute of Kyushu Imperial University,2, 241-276.

[13]Li Z C, Zhang H L, Cao Y S, Qiu Z E, Wei X H, Tang S X, YuP, Wang X K. 2003. Studies on the sampling strategyfor the primary core collection of Chinese ingeniousrice. Acta Agronomic Sinica, 29, 20-24.

[14]Liu K, Muse S. 2004. PowerMarker: New Genetic DataAnalysis Software. ver. 2.7. [2006-2-5]. http://www.powermarker.net

[15]Liu S, Cheng H, Wang H, Zhu Y G. 2002. DNApolymorphism of main restorer lines of hybrid rice inChina. Chinese Journal of Rice Science, 16, 1-5.

[16]Liu W, Shi Y L, Ma H W, Wang J, Li Z C, Zhang H. 2005.Study on heterotic ecotypes of Japonica rice based onthe heterosis. Acta Botanica Boreali-OccidentaliaSinica, 25, 64-69.

[17]Londo J P, Chiang Y C, Hung K H, Chiang T Y, Schaal B A.2006. Phylogeography of Asian wild rice, Oryzarufipogon, reveals multiple independent domesticationsof cultivated rice, Oryza sativa L. Proceedings of theNational Academy of Sciences of the United States ofAmerica, 103, 9578-9583.

[18]Mantel N. 1967. The detection of disease clustering and ageneralised regression approach. Cancer Research, 27,209-220.

[19]Melchinger A E, Lee M, Lamkey K R, Hallauer A R,Woodman W L. 1990. Genetic diversity for restrictionlength polymorphisms and heterosis for two diallelesets of maize inbreds. Theoretical and AppliedGenetics, 80, 488-496.

[20]Miller M P. 1997. Tools for Population Genetic Analyses(TFPGA) 1.3: A Windows Program for the Analysis of Allozyme and Molecular Population Genetic Data.[2006-6-5]. http://www.marksgenticsoftware.net/_vti_bin/shtml.exe/tfpga.htmNei M. 1987. Molecular Evolutionary Genetics. ColumbiaUniversity Press, New York.

[21]Nei M, Tajima F, Tateno T. 1983. Accuracy of estimatedphylcgenetic trees from molecular data. Journal ofMolecular Evolution, 19, 153-170.

[22]Oka H I. 1988. Origin of Cultivated Rice. Japan ScienceSociety Press, Tokyo.Panaud O, Chen X, McCouch S R. 1996. Development ofmicrosatellite markers and characterization of simplesequence length polymorphism (SSLP) in rice (Oryzasativa L.). Molecular Genetics and Gemomics, 252, 597-607.

[23]Pritchard J K, Stephens M, Donnelly P. 2000. Inference ofpopulation structure using multilocus genotype data.Genetics, 155, 945-959.

[24]Qi YW, Zhang D L, Zhang H L, Wang M X, Sun J L, WangM X, Sun J L, Wei X H, Qui Z E, Tang S X, et al. 2006.Genetic diversity of rice cultivars (Oryza sativa L.) inChina and the temporal trends in recent fifty years.Chinese Science Bulletin, 51, 681-688.

[25]Rohlf F. 1997. NTSYS-pc: Numerical Taxonomy andMultivariate Analysis System. Applied Biostatistics,Setauket, NY.Rosenberg N A. 2002. Distruct: A Program for theGraphical Display of Structure Results. [2006-7-2].http://www.cmb.usc.edu/~noahr/distruct.html

[26]Saitou N, Nei M. 1987. The neighbor-joining method: anew method for reconstructing phylogenetic trees.Molecular Biology and Evolution, 4, 406-425.

[27]Sano R, Morishima H. 1992. Indica-japonica differentiationof rice cultivars viewed from the variation in keycharacters and isozymes with special reference to landraces from the Himalayan hilly areas. Theoretical andApplied Genetics, 84, 266-274.

[28]Second G. 1982. Origin of the genic diversity of cultivatedrice (Oryza spp.): study of the polymorphism scored at40 isozyme loci. Japanese Journal of Genetics, 57, 25-57.

[29]Sokal R R. 1979. Testing statistical significance ofgeographic variation patterns. Systematic Zoology, 28,227-232.

[30]Stuber C W, Lincoln S E, Wolff D W, Helentjarisn T, LanderE S. 1992. Identification of genetic factors contributingto heterosis in a hybrid from two elite maize inbred linesusing molecular markers. Genetics, 132, 823-839.

[31]Takezaki N, Nei M. 1996. Genetic distances andreconstruction of phylogenetic trees from microsatelliteDNA. Genetics, 144, 389-399.

[32]Ting Y. 1957. The origin and evolution of cultivated rice inChina. Acta Agronomic Sinica, 8, 243-260.

[33]Vigouroux Y, Matsuoka Y, Doebley J. 2003. Directionalevolution for microsatellite size in maize. MolecularBiology and Evolution, 20, 1480-1483.

[34]Wang M X, Zhang H L, Zhang D L, Pan D J, Li D Y, Fan ZL, Qi Y W, Sun J L, Yang Q W, Li C, et al. 2008.geographical genetic diversity and divergence ofcommon wild rice (O. rufipogon Griff.) in China. ChineseScience Belletin, 53, 3559-3566.

[35]Weir B S, Cockerham C C. 1984. Estimation F-statistics forthe analysis of population structure. Evolution, 38,1358-1370.

[36]Wilcoxon F. 1945. Individual comparisons by rankingmethods. Biometrics Bulletin, 1, 80-83.

[37]Zhang D L, Zhang H L, Wang M X, Qi YW, Sun J L, WangF M, Wei X H, Han L Z, Qiu Z E, Tang S X, et al. 2009.Genetic structure and differentiation of Oryza sativa L.in China revealed by microsatellites. Theoretical andApplied Genetics, 119, 1105-1117.

[38]Zhang D L, Zhang H L, Wei X H, Qi YW, Wang M X, SunJ L, Ding L, Tang S X, Qui Z E, Cao Y S, et al. 2007a.Genetic structure and diversity of Oryza sativa L. inGuizhou, China. Chinese Science Bulletin, 52, 343-351.

[39]Zhang H L, Sun J L, Wang M X, Liao D Q, Zeng YW, ShenS Q, Yu P, Mu P, Wang X K, Li Z C. 2007b. Geneticstructure and phylogeography of rice landraces inYunnan, China revealed by SSR. Genome, 50, 72-83.

[40]Zhang H L, Zhang D L, Wang M X, Sun J L, Qi Y W, Li J J,Wei X H, Han L Z, Qiu Z E, Tang S X, et al. 2011. A corecollection and mini core collection of Oryza sativa L. inChina. Theoretical and Applied Genetics, 122, 49-61.

Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites

Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites

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