Identification and Purity Test of Super Hybrid Rice with SSR Molecular Markers

Abstract

Abstract: Five super hybrid rice combinations, i.e. HYS-1/R105, Pei’ai 64S/E32, Liangyoupeijiu (Pei’ai 64S/9311), 88S/0293, and J23A/Q611, and their parental lines were tested by means of SSR analysis. A total of 144 SSR primer pairs distributed on 12 rice chromosomes were used, out of which 47 detected polymorphism among the tested rice lines. Among all these primers, RM337 and RM154 produced polymorphic patterns in four or more of the tested experimental materials respectively, and they could distinguish among most rice genotypes tested. Twenty-four primer pairs, two on each rice chromosome, were selected to make a reference SSR marker-based fingerprinting for the rice lines. For most of the primer pairs, F₁ hybrids mainly showed complementary pattern of both parents, which could be very useful to distinguish the F₁from its parental lines. In addition, 5 primer pairs were selected as special primer pairs for five hybrid rice combinations respectively. By combining the rapid, simple method on DNA extraction, it is suggested that SSR technique has wide prospective in variety authentication and purity identification.

Key words: simple sequence repeats, molecular marker, super hybrid rice, identification, purity

XIN Ye-yun, ZHANG Zhan, XIONG Yi-ping, YUAN Long-ping. Identification and Purity Test of Super Hybrid Rice with SSR Molecular Markers
[J]. RICE SCIENCE.

References

1 Zhao Z Q, Zheng H L, Zhang C G. Development of molecular markers and their application in botany research. Fujian Sci&Technol Trop Crops, 2000, 25(4): 13–16. (in Chinese with English abstract)

2 Fang X J, Liu S H, Jiang S Y. Progress on identification of seed purity and authenticity using DNA molecular markers. J Agric Biotech, 2000, (2): 106–110. (in Chinese with English abstract)

3 Liang M S, Zeng Y, Zhou X, Hou L J, Li X. Genetic markers and their applications in identifying crop cultivars. Chinese Bull Bot, 2001, 18(3): 257–265. (in Chinese with English abstract)

4 Williams J G, Kubelik A R, Livak K J, Rafalski J A, Tingey S V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res, 1990, 18(22): 6531–6535.

5 Chen H, Chen M L, Zhu L H, Qian Q, Min S K. Purity identification of hybrid rice Shanyou 63 by RAPD method. Chinese Sci Bull, 1996, 41(9): 833–836. (in Chinese)

6 Chen Y H, Jia J H, Li C Y, Jin D M, Wang B. Rice seed ientification by computerized AFLP-DNA fingerpringting analysis. In: Prospects on Rice Genetics and Breeding for the 21^st Century—International Rice Genetics and Breeding Symposium. China Agricultural Science and Technology Press, 1999. (in Chinese with English abstract)

7 Panaud O, Chen X, McCouch S R. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 1996, 252(5): 597–607.

8 McCouch S R, Chen X, Panaud O, Temnykh S, Xu Y, Cho Y G, Huang N, Ishii T, Blair M. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol, 1997, 35(1-2): 89–99.

9 Wu K S,Tanksley S D. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet, 1993, 241: 225–235.

10 Akagi H, Yokozeki Y, Inagaki A, Nakamura A, Fujimura T. A codominant DNA marker closely linked to the rice nuclear restorer gene, RF-1, identified with inter-SSR fingerprinting. Genome, 1996, 39(6): 1205–1209.

11 Yang G P, Maroof M A, Xu C G, Zhang Q, Biyashev R M. Comparative analysis of microsatellite DNA polymor- phism in landraces and cultivars of rice. Mol Gen Genet, 1994, 245 (2):187–194.

12 Li L, Yang J B, Wang X F. 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. (in Chinese with English abstract)

13 Yu Y H, Li Y H, Ma R R, Wang X Y, Hu G C, Si H M, Fu Y P, Sun Z X. Establishment of fingerprint map of Ning 2A with simple sequence repeat markers. Chinese J Rice Sci, 2001, 15(3): 216–217. (in Chinese with English abstract)

14 Zhan Q C. Studies on identification of purity and factuality of hybrid rice seed using microsatellite marker. Hybrid Rice, 2002, (5): 46–50. (in Chinese with English abstract)

15 Peng S T, Zhang J Y, Yan Q C, Zheng K L. SSR marker selection and purity detection of major hybrid rice combinations and their parents in China. Chinese J Rice Sci, 2003, 17(1): 1–5. (in Chinese with English abstract)

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