Mapping a Novel Gene of Cold Tolerance at Booting Stage by Using Near-Isogenic Lines in japonica Rice

Abstract

Abstract: Genetic analysis showed that cold tolerance at booting stage of near-isogenic lines (NILs) of Kunmingxiaobaigu was controlled by a gene with large phenotypic variance. One hundred and sixty-four simple sequence repeats (SSR) distributed over 12 chromosomes were used to screen polymorphism between Towata (recurrent parent, RP) and near-isogenic line pool (NILP), and two SSR markers at the long arm of chromosome 5 showed polymorphism in comparison with RP genome. Of the two markers, RM31 was found possibly linked with the cold tolerance gene at booting stage through one-way ANOVA. Twelve SSR markers around RM31 were then used to detect polymorphism between RP and NIL, and only RM7452 had polymorphism. The gene of cold tolerance at booting stage was further mapped on chromosome 5 between RM7452 and RM31 with genetic distances of 4.8 cM and 8.0 cM, respectively. This gene explained 10.50% of phenotypic variance and 5.10% of phenotypic variance of fully filled grains, and was tentatively designated as Ctb(t).

Key words: booting stage, near-isogenic line, simple sequence repeat, genetic analysis, cold tolerance gene

SHEN Shi-quan, ZENG Ya-wen, LI Shen-chong, WEN Guo-song, PU Xiao-ying . Mapping a Novel Gene of Cold Tolerance at Booting Stage by Using Near-Isogenic Lines in japonica Rice[J]. RICE SCIENCE, 2005, 12(3): 163-167 .

References

1 Shen S Q. Evaluation and genetic research of near-isogenic lines for cold tolerance at booting stage of Yunnan japonica rice. Master Disseration. Beijing: China Agricultural University. 2003. (in Chinese with English abstract)
2 Zeng Y W, Shen S Q, Ye C R. Development of near-isogenic lines for cold tolerance in rice. Chinese Sci Abstr, 1999, 5(8): 1084–1085. (in Chinese)
3 Dai L Y. Researching of germplasms with cold tolerance resources in Yunnan rice genetic resources. PhD Dissertion. Wuhan: Huazhong Agricultural University. 2001. (in Chinese with English abstract)
4 Zeng Y W, Ye C R, Shen S Q. Breeding and genetic research of near-isogenic lines for cold tolerance at booting stage in rice. Progr Nat Sci, 2001, 11(1): 94–96. (in Chinese)
5 Muehlbauer G J, Specht J E, Thomas-Compton M A, Staswick P E, Bernard R L. Near-isogenic line—a potential resource in the integration of conventional and molecular marker linkage maps. Crop Sci, 1988, 28: 729–735.
6 Murray M G, Thompson W F. Rapid isolation of high molecular weight plant DNA. Nucl Acids Res, 1980, 8: 4321–4325.
7 Temnykh S, Park W D, Ayers N, Cartinhour S, Hauck N, Lipovich L, Cho Y G, Ishii T, McCouch S R. Mapping and genome organization of microsatellite sequence in rice (Oryza sativa L.). Theor Appl Genet, 2000, 100: 697–712.
8 Saito K, Miura K, Nagano K, Hayano-Saito Y, Araki H, Kato A. Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length. Theor Appl Genet, 2001, 103: 862–868.
9 Saito K, Miura K, Nagano K, Hayano-Saito Y, Saito A, Araki H, Kato A. Chromosomal location of quantitative trait loci for cool tolerance at the booting stage in rice variety “Norin-PL8”. Breeding Sci, 1995, 45: 337–340.
10 Kato A. Analysis of the genetic loci involved in cool tolerance of a cool-tolerant rice strain Hokkai PL5. Breeding Sci, 1997, 47(2): 114–119.
11 Andaya V C, Mackill D J. QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica × indica cross. Theor Appl Genet, 2003, 106: 1084–1090.
12 Yoshinobu T. Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate rice. Breeding Sci, 2001, 51(3): 191–197.
13 Liu F X, Sun C Q, Tan L B, Li D J, Fu Y C, Wang X K. Mapping the gene of cold tolerance at booting stage of
14 Jiangxi Dongxiang Oryza rufipogon Griff. Chinese Sci Bull, 2003, 48(17): 1864–1867. (in Chinese)
15 Li H B. Genetic basis of low-temperature-sensitive sterility in indica-japonica hybrids of rice as determined by RFLP analysis. Theor Appl Genet, 1997, 95: 1092–1097.
16 Ye C R, Dai L Y, Yang Q C, Kato A, Saito K, Ise K. QTL analysis of cold tolerance at the booting stage in Yunnan rice variety Chongtui. Chinese J Rice Sci, 2001, 15 (1): 13–16. (in Chinese with English abstract)

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