Construction and Testing of a Primary Microsatellite Database of Major Rice Varieties in China

摘要/Abstract

摘要： Sixty-three major inbred varieties and parental lines of major F1 hybrids used in the commercial rice production in China were assayed with rice microsatellites screened in a previous study and additional microsatellites on four chromosomes. A set of 24 markers was selected and proposed for its application in the variety identification of rice, which are distributed on all the 12 rice chromosomes with 2 markers on each chromosome. The 63 major varieties and parental lines, as well as 41 major F1 hybrids, were genotyped with the markers. Alleles detected in each line at each marker locus were verified. By matching marker genotypes of corresponding F1, maternal and paternal lines of hybrid rice, high reliability of the maternal lines was verified, data on the paternal lines were modified, and a false hybrid was removed. A database containing genotype data of 103 major rice varieties and parental lines at the 24 marker loci was constructed and analyzed.

关键词: simple sequence repeat, rice (Oryza sativa), variety identification, frequency of polymorphism, database

YING Jie-zheng, SHI Yong-feng, E Zhi-guo, ZENG Rui-zhen, CHEN Jie, ZHU Zhi-wei, ZHUANG Jie-yun . Construction and Testing of a Primary Microsatellite Database of Major Rice Varieties in China[J]. RICE SCIENCE, 2007, 14(4): 247-255 .

参考文献

1 Garland S H, Lewin L, Abedinia M, Henry R, Blakeney A. The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.). Euphytica, 1999, 108: 53–63.
2 Karakousis A, Barr A R, Chalmers K J, Ablett G A, Holton T A, Henry R J, Lim P, Langridge P. Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm. Aust J Agric Res, 2003, 54: 1197–1210.
3 Leigh F, Lea V, Law J, Wolters P, Powell W, Donini P. Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica, 2003, 133: 359–366.
4 Singh R K, Sharma R K, Singh A K, Singh V P, Singh N K, Tiwari S P, Mohapatra T. Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica, 2004, 135: 135–143.
5 Tommasini L, Batley J, Arnold G M, Cooke R J, Donini P, Lee D, Law J R, Lowe C, Moule C, Trick M, Edwards K J. The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor Appl Genet, 2003, 106: 1091–1101.
6 Bredemeijer G M M, Cook R J, Ganal M W, Peeters R, Isaac P, Noordijk Y, Rendell S, Jackson J, R?der M S, Wendehake K, Dijcks M, Amelaine M, Wickaert V, Bertrand L, Vosman B. Construction and testing of microsatellite database containing more than 500 tomato varieties. Theor Appl Genet, 2002, 105: 1019–1026.
7 R?der M S, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke R J, Vosman B, Ganal M W. Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet, 2002, 106: 67–73.
8 Li L, Yang J B, Wang X F, Xiang T H, Wu J D. Identification of Xieyou combinations of hybrid rice and their three parents by using RAPD and microsatellite markers. Chinese J Rice Sci, 2000, 14(4): 203–207.
9 Li J B, Mu T M, Xia J W, Fang X J. Seed purity identification of a two line hybrid rice combination Liangyoupeisheng based on microsatellite markers. Chinese Agric Sci Bull, 2002, 18(6): 10–13. (in Chinese with English abstract)
10 Su S Z, Huang Y B, Yang J P, Ding Z F, Gao S B. The study of testing the seeds purity of hybrid by SSR. Seed, 2003, 127(1): 23–25. (in Chinese with English abstract)
11 Xin Y Y, Zhang Z, Xiong Y P, Yuan L P. Identification and purity test of super hybrid rice with SSR molecular markers. Chinese J Rice Sci, 2005, 19(2): 95–100. (in Chinese with
English abstract)
12 Nandakumar N, Singh A K, Sharma R K, Mohapatra T, Prabhu K V, Zaman F U. Molecular fingerprinting of hybrids and assessment of genetic purity of hybrid seeds in rice using microsatellite markers. Euphytica, 2004, 136: 257–264.
13 Xiao X Y, Wang Y P, Zhang J Y, Li S G, Rong T Z. SSR marker-based genetic diversity fingerprinting of hybrid rice in Sichuan, China. Chinese J Rice Sci, 2006, 20(1): 1–7. (in Chinese with English abstract)
14 Shi Y F, Ying J Z, Wang L, Zhu Z W, Zhuang J Y. Screening SSR markers for rice variety identification. Chinese J Rice Sci, 2005, 19(3): 195-201. (in Chinese with English abstract)
15 Zheng K L, Huang N, Bennett J, Khush G S. PCR-based marker-assisted selection in rice breeding. IRRI Discussion Paper Series. No. 12. Manila: International Rice Research Institute, 1995.
16 Lu Y J, Zheng K L. A simple method for isolation of rice DNA. Chinese J Rice Sci, 1992, 6(1): 47–48. (in Chinese)
17 Zhuang J Y, Qian H R, Zheng K L. Screening of highly- polymorphic RFLP probes in Oryza sativa L. J Genet & Breeding, 1998, 52: 39–48.
18 Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA, 1979, 76: 5269–5273.
19 NTSYSpc Version 2.11Q. Copyright (C) 2000-2003, New York: Applied Biostatistics Inc, 2000–2003.
20 Ying J Z, Shi Y F, Zhuang J Y, Xue Q Z. Microsatellite marker evaluation on genetic diversity of the major commercial rice varieties in China. Sci Agric Sin, 2007, 40(4): 645–654. (in Chinese with English abstract)
21 Wu J L, Shi Y F, Chen J, Vera Cruz C, Zhuang J Y, Leung H, Zheng K L. Source and inheritance of the within cultivar residual variation detected in an indica rice variety IR64. Rice Sci, 2007, 14(1): 21–26.
22 Olufowote J O, Xu Y, Chen X, Park W D, Beachell H M, Dilday R H, Goto M, McCouch S R. Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome, 1997, 40: 370–378.
23 Shu Q Y, Wu D X, Xia Y W, Gao M W, Ayres A, Larkin P D, Park W D. Microsatellite polymorphism on the Waxy gene locus and their relationship to amylose content in indica and japonica rice, Oryza sativa L. Acta Genet Sin, 1989, 26(4): 350–358. (in Chinese with English abstract)
24 Yashitola J, Thirumurugan T, Sundaram R M, Naseerullah M K, Ramesha M S, Sarma N P, Sonti R V. Assessment of purity of rice hybrids using microsatellite and STS markers. Crop Sci, 2002, 42(4): 1369–1373.
25 Cheng B Y, Shi Y F, Shen W F, Zhuang J Y, Yang S H. Microsatellite marker-based analysis of rice varieties in National Regional Yield Trial of Southern China. Chinese J Rice Sci, 2007, 21(1): 7–12. (in Chinese with English abstract)

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